Rejected Routes

Exactly what it sounds like. Route ideas that didn't make the cut.
In the beginning, the plan was for Fate/stay night to have four different routes, one for each heroine.
It would start off by letting the player arbitrarily choose between playing as either Shirou or Rin. Then around the middle of the story they would finally meet, and after that you would branch off into one of the four routes for the last half of the game. Yeah, I don't really understand how it was going to work either.
Anyway, getting back to the rejected routes, it goes without saying that the Illya route tops the list.
Besides that, there was also the “Rider route where you fight against Rin and Saber,” and the “Caster route where Caster gets turned into a loli and becomes your partner.”
While all traces of the Caster route were completely erased, the development where you teamed up with Rider was actually folded into part of the final story.
If the Illya route had made it into the game, the diversion point probably would have been on the ninth day of the Sakura route. Instead of choosing between being a superhero and choosing Sakura, there would be a third choice where you could choose Illya.
But unfortunately, as it stands that choice doesn't exist.

Fate/side material: Fate Encyclopedia