Prototype Shirou/Ayaka was apparently an actual mage, and was aware of the nature of the Grail War from the start. We see her using an ofuda-based ward and shooting black feathers, the latter of which seems to impress Lancer somewhat (he whistles and calls it "black magic from ancient times" - given that Cu Chullain was a mage himself, we can probably take him at his word).
Prototype Kotomine is some kind of perverted sleazebag preacher instead of the badass we all know and hate.
Lancer wears something that more closely resembles armor than the tight blue bodysuit. Or maybe he's wearing it
over the TBB.
Both Archer and Gil as they appear in F/SN look to have been based on the same Prototype Archer. Makes sense, given their similarities.
Prototype Archer's Noble Phantasm takes a much more... literal interpretation of "Star of Creation that Split Heaven and Earth".
