-The original villainous priest was some white guy that was racist against Japanese people with Berserker as his Servant. He was still the eighth Master, but his Berserker was summoned in the current war, not the past. Berserker was still Hercules. This character was scrapped, Kirei Kotomine created and put in his place, and Berserker made into new character Ilyasviel's Servant instead.
-Current Archer was going to be Gilgamesh instead of who Rin's Archer is. His abilities included a blend of both current Gilgamesh and Rin Archer's abilities (Gate of Babylon while also being a skilled close ranged fighter that dual wielded swords and had a bow). He had a different Noble Phantasm, but it was still EX ranked and still OP. He was less overpowered than canon Gilgamesh though, since he was meant to be a rival instead of the villain. His personality was more amiable as a result (as you'd probably expect given the ending to the Epic of Gilgamesh). While canon Gilgamesh views Saber as a possession, Proto Gilgamesh legitimately fell in love with Ayaka and thought of her as a person. After Kirei and Shirou were created, Nasu and/or Takeuchi decided to bump Gilgamesh up to main villain, have him be summoned from the past war, and split his abilities between Rin's Archer and canon Gilgamesh. As a result his power level was increased and Gate of Babylon became more emphasized and powerful as well (originally it could only fire 10 weapons at a time, but it was still rapid fire). His personality was then darkened and his pride even more emphasized, presumably since he'd be unbeatable otherwise, as he is in all of his non-F/SN appearances. His Noble Phantasm would've been based on the Great Flood instead of Enuma Elish, with the former having much more association with Gilgamesh than the latter (as the earliest telling of a worldwide flood is in a story told to Gilgamesh within the Epic).
-Rin's backstory was different and her personality somewhat darker.
-Rin had Lancer as a Servant instead. He was still Cu Chuliann.
-Due to having a proper Master, his stats were MUCH higher, because seriously, go look up who the [radio edit] Cu Chuliann is sometime. He's literally pretty much Ireland's Hercules.
-Rider was Perseus, instead of who she is now. To be clear, it wasn't a genderbent Perseus.
-Assassin was ACTUALLY Kojiro Sasaki, instead of just a "close enough" guy. As stated in the VN itself, an "actual" Kojiro doesn't exist in canon.
-Excalibur was stronger in Prototype (Rank EX), but had 13 restrictions, among which were "the fight must be honorable" and "the opponent must be stronger" making it harder to use. Incidentally, Saber's fight with Archer (remember, he's Gilgamesh here) would have met all 13 of these requirements.
-Saber's past Master would have been Ayaka's older sister Manaka (rather than the father/son relationship Kiritsugu and Shirou have). She knew the Grail was evil and planned to make use of it anyway because why not? She was madly in love with Saber and wanted the Grail to save his kingdom. She sacrificed innocents to the Grail, including her own father, and would have sacrificed Ayaka had Saber not turned on her and killed her. Like Kirei, however, she survived due to the Grail's taint. Once Kirei and Ilya were created as separate characters, her traits were split among them. Due to her death and resurrection, she doesn't age and is thus locked as psycho loli despite being the older sister.
-This means that Saber also knew the Grail was evil from the start, and as such his relationship with Ayaka was completely different from Shirou/Saber.
-Instead of being corrupted at some point like in F/SN, the Grail was originally going to be evil from the start, and it's true purpose would be to summon the Beast of Revelation.

-Rin dies from a curse (in which the pain increasingly gets worse) she harbored from the beginning of the story. She makes Lancer promise to kill her once she can't bear the pain anymore, but he is unable to bring himself to do it. Her death is what leads to him helping the heroes. And to be clear, no, Rin has no such curse in F/SN.
-Saber would've been stolen by evil priest guy instead of Caster. Who was still Medea.
-Lancer would fight Saber and Berserker at the same [radio edit]ing time instead of just fighting Archer like in canon. I do not know if Lancer would survive this fight, but Saber and Berserker both would.
-Canon Saber is actually quite a bit stronger then Arthur in terms of statistics...when she has a proper Master, anyway. Sans, again, Excalibur.
-Gilgamesh vs Hercules would still happen, and it'd a mix between the Fate route battle of Archer vs Berserker and the UBW route version of this clash. It would've been a MUCH more even fight due to Gilgamesh's lower power level, and he'd technically lose the fight and survive, while Hercules would win but die. Gilgamesh was specifically chosen to be in the story to be a strong obscure hero that could take on the famous Hercules in an even fight, so that this got watered down in the final version bugs me. The other candidate for this purpose, India's hero Karna, later got created and used in Fate/Apocrypha and Fate/Extra CCC.
-The Rin vs Caster fight would've been Ayaka vs priest guy, except she'd win and kill him, thus getting Saber back. This and Gilgamesh's slaying of Hercules would then be the plot twist that causes main villain Manaka to take center stage.
-Manaka would use the Grail to summon the six heroes that she and Saber killed in the previous Grail War as her Servants. The Lancer is the Valkyrie Brunhildr. Rider probably would've been Alexander the Great, who actually remained in canon and was used in Fate/Zero. Presumably the story from here would've been "Arthur and Gilgamesh have to team up and beat these 6 Servants before facing final boss Servant Beast." If Lancer survived fighting Arthur/Hercules he'd probably end up helping too.

-Perseus would've a similar relationship with his Master that Sakura and Rider did, except his Master already died (he was terminally ill) but used his Command Spells to permanently incarnate Perseus, much like Gilgamesh is in canon (pretty sure Command Spells can't do this anymore). Thus, Perseus would fight to win the Grail and wish his Master back to life. Like canon Rider, he'd do evil deeds like eating souls to maintain his mana in order to do this.
-That said, he would've been one of Ayaka's classmates like Shinji is to Shirou, except more like an actual friend. He'd end up saving Saber and Ayaka from Caster at one point.
-He had a Pegasus as a Noble Phantasm like current Rider does. Perseus no longer has this Noble Phantasm in canon.
-When Arthur is stolen by the evil priest, he gets corrupted like Saber does after the Shadow eats her, for some reason. The corruption goes away once Ayaka gets him back.
-At some point after Perseus was changed to Medusa, it would be decided that Hercules would kill her after she killed him a few times with her Noble Phantasm. I don't know if Perseus would've also had this fate.

Archer being Shirou as a heroic spirit.

I don't know where in Day 15 that is, but I got it right before Shirou goes to fight Archer in the cathedral, when he kidnaps Rin. And yeah, it was a great twist for me, too.

said "Trace, On!"

So basically, it's close to the same thing as the first h-scene in the Fate route. >_>

Emiya confirmed for Berserker class.

You mean, character-breakingness on Rin's part? Yes.

Because Rin is totally going to be helpless and passive in bed while Shirou basically violates her. Yes, because that's totally believable.

Nasu PLS