I'm pretty sure Shirou Emiya is a pretty fascinating character, the reason he saves people isn't because it's the right thing to do but because saving people is basically the only thing that makes him feel happy, he doesn't save people because he wants to, he saves people because he needs to.
Archer is his future self, he basically lived the rest of his life saving people for a single wish, he wanted to smile the same way Kiritsugu smiled when he was saved by him.
in the end he got executed by the people he saved and he wasn't even able to die in peace, due to his contract with the counterforce he's basically forced to kill the few to save the many, he basically died and went to his own personal hell.
So yes, Shirou Emiya isn't just some random audience insert, he's a completely fleshed out character, the VN would still be good without the sex scenes or even the love interest, I'd go as far as to say that the sex scenes in the vn felt like it was put in at the last second.