Gilgamesh's death, but the meta issues around it (HF more or less has Sakura stomp over Saber and Gilgamesh's plots, much like how Kariya's plot in F/Z ultimately amounted to nothing compared to the Saber/Kiritsugu and Kirei/Gilgamesh ones), as well as the fact that he's a better character in F/Z and got to be awesome there anyway

Saber Alter and Dark Sakura?

Kirei being generally hugely more badass in general yes, but what really cinched it was when he said that he only wants to find out how Avenger will react to his actions -- and this would be a question to all those like Kirei, who are born defected and unwanted by the world. Shirou says that Kirei is unwavering in an ideal, but here it just came down to a simple loneliness, and a desire to have someone else like you, who understands (not that Kirei would ever phrase it that explicitly). That put plenty of depth on Kirei's character for me.

Saber Alter was interesting in a kind of thought-experiment type thing, but there wasn't the huge tension to it I was expecting. Peytral told me to choose wrong in the confrontation with Rider so I got to see THAT awesome scene of Shirou going head-to-head with Saber, and I think that was an awesome way of resolving that conflict. And an Excalibur of darkness was badass -and I do remember mentioning how King Arthur frequently rode out in a knight of black armour to challenge his knights anonymously, and you mentioning that that was kinda used in F/SN. So if that was a reference, I do appreciate that.
Dark Sakura I was really really impressed with, both in terms of design and in precept. It's critical that Sakura is doing that of her own will, I think, otherwise it just becomes standard "oh noes love interest possessed by evil" -- and again, the scary thing is that it's plausible, and Sakura still retains enough of her previous self to be ashamed of some of her actions, even as she pursues them -- that contradiction is pretty compelling, I thought.
Also, her killing Assassin and then reaching into her own heart to rip out Zouken was sooooo badass.
And again, the battle of infinite vs. limitless against Tohsaka was freaking amazing

Actually no, but Saber/Emiya. What annoyed me about that ship in Fate was that it was a ship of similarities, but not equals: one on hand, King Arthur at the end of her life, who is a heroic spirit, and on the other, a derpy teenage boy who spends most of the route trying to keep King Arthur in the kitchen.
But the idea of one "endlessly pursuing" and one "endlessly waiting" - the latter playing nicely into the whole "King Arthur sleeps until s/he is needed" dealio - puts them on equal footing, and all the labours/infinite work that Emiya undergoes makes him equal to King Arthur, I think -- and the idea of a love that perseveres despite that is wonderful. The integrity of both their ideals/characters is maintained -- and I think that more than anything is a wonderful conclusion for a certain Archer.
If you actually haven't seen this yet, the last episode's on Youtube - just click the part 3 of 3, the other two are just recaps of the Fate route.

Well, the mud does blacken Saber and Sakura, but yeah, their actions are still their own, they're not slaves to Avenger. The mud being a corruption rather than possession is the thing that makes it interesting. Berserker Alter was apparently able to resist the mud better than Saber because "Hercules has often felt the pain of going berserk and has a strong heart," or something like that, which I guess kind of makes sense since given what we already know about them, and, well, him being Hercules. Above all, though, of course, it's just satisfying to see Sakura finally make an ACTIVE reaction to her experiences instead of taking them passively, regardless of the consequences of her actions.

And, of course, the fact that the mud didn't blacken Gilgamesh at all and only affected part of his personality is a testament to his own character as well. Actually, if Shadow!Sakura didn't digest him immediately, he would've actually torn his way back out, so yeah.

While some people feel Last Episode kind of ruins the Fate route's ending, (and it is only in there mostly because of Takeuchi asking Nasu for it) I actually liked it because I feel it did what Fate as a whole was trying to do much better. That is, Saber as Arturia the girl, not King Arthur. And as you said, Shirou had to work his way up as a hero, so they met each other at their own levels, instead of being at opposite ends in terms of experience.

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Above all, though, of course, it's just satisfying to see Sakura finally make an ACTIVE reaction to her experiences instead of taking them passively, regardless of the consequences of her actions.

Yes, precisely! That's why I enjoyed it so much - I actually kinda didn't want her to be cured entirely, since shadow!Sakura is so much more interesting than normal Sakura. At least in the epilogue she becomes the manager of Fuyuki, so that's something.
While we're talking about activity vs. passivity, <_< the sex scenes. I always watch them because there might be character stuff/symbolism there (KS did this really well with Shizune and Hanako, the former being silence/sound and the latter for character reasons), but my God the sex scenes are awful in general - no matter the character, as soon as they're on the other side of Shirou they turn into passive, bashful, and shirking violets, protesting NO, NO as Shirou quasi-rapes them. <_< At least in Sakura's route, she's as desirous and "normal human being" as Shirou, even if it's handwaved as "oh, this lewd body" - because heaven forbid women want to have sex. <_<
Saber scene 2 is actually a little better for this.

Complete non-sequitur (man I can never spell that), but on the topic of Ilya's awesomeness: the pinnacle of her two identities, as Grail and as herself, were both awesome. Talking to Zouken and making him remember what he started from (which is in itself amazing, Zouken is like Shirou 500 years later), and then closing the Greater Grail. The whole "I'm a bit older, so it's the duty of the older sister to protect the younger brother" was incredibly sweet, and definitely the height of Ilya's badassness. That was handled so well.

I actually probably liked the ending of Unlimited Blade Works the least of the three - and by ending I mean the final arc in general. Saber's fight vs. Assassin was great, but in general I thought that route climaxed with the vs. Archer fight earlier, where Shirou overcomes his future self. That was so amazing and so well-done, and emphasized that it was such a hard fight, that there's not a whole lot of tension after that -- I never for a moment doubted that Shirou would beat Gilgamesh, because of how much the story is all about CONVICTION and IDEALS, so now that Shirou has his resolution, backing from Tohsaka, and the knowledge from Archer, the tension inadvertently is gone from that scene and it's just a big sprezzatura about how awesome Shirou is.
Also, if Shirou was projecting the NPs as Gilgamesh uses them, how is projection faster than retrieval? <_< They've already been retrieved.
And on the endings: I got the Normal Ending first, and I found that was better than the True Ending. Sure it's sad not having Saber, but it's more serious and "profound" in tone, I think. Tohsaka in the sunset saying "You're mine," and dragging Shirou to the Clock Tower - and making him say that he wants it. It's the kind of assertive Tohsaka that'd been missing so much in the route.
Having Saber stick around is still good, though~

Similarly, I -almost- prefer the normal ending to the True ending (if I could somehow still keep the Ilya badassness...). The True ending is happy - but that's the thing, it feels almost too happy, and too neatly concludes everything. There's a bittersweet weight in the Normal ending that calls out to the reader - it leaves so much unresolved, which creates that kind of ache that says "No, life should be better than this," it can't end this way (with Sakura wasting away her life planting flowers). It's much more elegaic, and I think it was definitely more moving, even if the True ending made me happy.
Two more things on the True ending:
1) I wish Fate/Stay Night shifted perspectives more often. Seeing Shirou through Tohsaka's eyes and seeing what his facial expressions are would've been nice to have a while ago.
2) DAAAAAAAAAAAMN Rider is so sexy

Well Saber's from a time period where women were like prizes/trophies to be won over and have sex with, right? She clearly doesn't think of herself as a woman when she's all in king mode, so once she tries to act her gender, wouldn't it make sense for her to be more passive?

As for Sakura, she's Japanese, and they're more traditional in their gender roles, again, see Aoi. Considering even the west has a stigma against women that love sex, I'd imagine Japan has it even more. And, of course, Nasu is Japanese, so that might just be the whole cultural difference there with what he grew up with and currently lives with, who knows.

And, of course, he sucks at writing porn. If you think this is bad, this is after he improved. The H scenes in his earlier work, Tsukihime, was even worse.

"I wanted Ciel to let Shiki use all of her holes to show how forgiving she is."

NASUUUUUUUUUUUUUUUUUUUUUUUUUU

Actually the ending where Saber stays is the Normal End, and the ending where she leaves is the True End, so there you go, you have what you want there. What I like of the UBW ending though is just the sheer badassery of Shirou vs Gilgamesh in the action-y sort of way, not so much the plotness of it. The awesome plot part was all about Archer getting resolution; the fact that he passes out in the True End while Rin talks to Archer more or less makes it focus on that.

As for Shirou vs Gilgamesh, the swords are all already there so Shirou can just grab them from the ground, while Gilgamesh has to deploy his, THEN grab them. Shirou can also just project mid-swing, while Gilgamesh has to, again, wait for the weapons to deploy before grabbing them. He can also draw the swords to his hand mentally kind of like that Jedi stuff in Star Wars, so that's another advantage he has. It's not a big time difference, but considering projection copies some of the skill of the original user of the weapon, it's enough that Gilgamesh is going to get beaten back if he can't prepare himself since he didn't practice with any of his weapons except Ea.

Though yeah, some people do come away from that scene thinking "lolGilgamesh can't melee" so yeah, I guess it could've been written better.

Funnily enough Nasu was originally going to have the Normal End be the True End and have the Normal End be a happy one but he ultimately "lost to the story," not quite sure what he means by that, but he also basically said that with all the darkness that's in Heaven's Feel, he couldn't bring himself to not make a happy ending. I myself prefer the True End because it feels like it was earned, whereas UBW's Good End is kind of just, yeah. I mean, Saber has enough mana to stay so it's perfectly plausible, but it just feels kind of TOO happy. That said, the Normal End, depressing as it is, isn't bad at all.

And yes, Ilya's sacrifice in the True End was the single best moment of her character, especially since Shirou had said the same thing to her earlier (I'm the big brother, so it's my job to protect my little sister vs her flipping it around since she's actually the older one). And, of course that smile ;~;

Saddest part in the route for me was that Ilya death.

Oh, and yeah, post-HF Sakura is supposed to be more forceful/takes after Rin a bit more, so she developed out of being a doormat, at least.

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Well Saber's from a time period where women were like prizes/trophies to be won over and have sex with, right? She clearly doesn't think of herself as a woman when she's all in king mode, so once she tries to act her gender, wouldn't it make sense for her to be more passive?

Well, The Morte d'Arthur, aka where we get the tale as we know it from, is actually filled with some pretty active women. Guinevere is moreso pursuing Lancelot than the other way around, though she does need to be rescued pretty often. Elaine's probably the most passive one -- she's obsessed with Lancelot, but even that is active and desiring, and she spends most of her time cleaning his wounds, even sneaking out to do so.
The middle ages has this polarized view of women in that you are either passive/chaste/pure, or you are a feared witch/desiring (women were considered closer to magic). Figures like Guinevere and Isolde more or less move in-between these categories, as they are active and desiring, political and hold power, and complex figures (even if still herp derp always need rescuing).

If Saber showed strain from trying to act her gender/contrary to her real self, then I could buy that, but I think it comes a bit too naturally to her. I mean, she snaps at Shirou and says "I thought you at least would understand," but then just stands on the bridge forlornly after he leaves, until he comes and gets her? How passive can one get? <_<
And didn't Nasu say that he made Shirou so "stay in the kitchen" to Saber because he wanted to remind the reader that Saber was a girl? <_< If the only way you can express femininity is by staying in the house... yeah.

Oh, I'm not saying it's a not expression of Japan's patriarchal culture. <_< It is, sadly. But I think literature at its best should challenge and overturn aspects of the status quo and cause perspectives to shift, and express the best of humanity. Rather than accepting that women should remain in the kitchen, I think Nasu should've challenged that.
-- I do have to grant him this, though: that in making King Arthur a woman, and keeping as much of Arthur's character as he did, Nasu already hurls a considerable challenge to the status quo/forces a rethink of that myth. This aspect is one that's easy to overlook because it's so self-evident, but it's one of the things that drew me to the Fate series.
Mind, that all was only mostly mid-route, and Shirou does overcome his delusions of trying to change Saber, and ultimately accepts her as a knight.

Yeah, that was my whole idea; not that there weren't any active women, but that society back then viewed passive women as the norm and ideal, and active women were a rarity or a bad thing. I mean, nobody's going to call Guinevere seducing Lancelot "good" when it goes and helps lead Camelot to it's downfall, for example. Of course Nasu's comment about "I wanted people to know Saber's a girl aside", I dunno his intent with that stuff, that's just my admittingly quickly thought out idea about that because while I can understand why the passiveness bugged you since you came off of KS, reading too deeply into Nasu's H scenes won't get you much of anywhere, lawl. Since the real reason behind it is 99% likely to be "Nasu sucks at porn," but otherwise you either take the flimsy reasoning or you just ignore it as out of character.

Oh uh and the fact that Takeuchi decides what goes into the H scenes and Nasu just writes them.