In one of the Tiger Dojos, Ilya mentions that it would be nice to see a Route in which Shinji cooperated with Shirou, or one Route when Caster became an ally. Taiga right away smacks Ilya in the head and say "Don't talk about the rejected Routes!". Along with the information on the "Ilya Route", which was cut and reworked into the "Heaven's Feel" route because Ilya is the Token Mini-Moe, this means that there would be a lot of Routes, but thanks to "time and resources not being infinite" (another quote from Taiga) they were rejected.
To be more specific, Fate/side material revealed that in the Caster Route, Caster would have reversed her age, turned into a loli and become the protagonist's partner. Unlike Rider's route which was also scrapped, none of this was incorporated in the end product.