I've found On Wings of Steel to be pretty engaging. It's definitely a different take on the crossover. It doesn't seem to be based on any of the particular endings to the game. It alludes a few times to something else having happened afterwards (or maybe some alternate ending that's not from the game?), the end result of which is that Shirou is the only one of the characters from F/SN who is still alive.
I've been enjoying Fear the Superhero by xolef225 (updated today to chapter 14) for similar reasons.