All I'm hearing is "I don't like Zero because Gen was mean to my waifu." Which is fine, I guess. It's just a silly hill to die on. Saber is the face of the franchise, so it obviously didn't hurt her stock too much. You can enjoy her in several other incarnations and mediums.
Unpopular opinion of my own:
I'm glad we don't have an Illya route.
She works better as a tragic figure, a microcosm of all that is wrong with magi society valuing results over the people trampled along the way. Sakura suffers in much the same way, but she has the potential for a happy ending, which takes the edge off. Even Saber gets a good conclusion in three of the five endings. That Illya always gets the short end of the stick gives her tragedy a permanence and a power that a lot of these other sub-plots lack. Illya can't ever be truly saved, and I wouldn't have it any other way.
I also never would have touched FSN if it had loli sex scenes.