I had a bit of an issue with Snape/Lily, myself, but I'm not sure if it's the portrayal of the crush or the very idea of it that rubbed me the wrong way. Something just...did.

Same here. I think that at least part of it is that it wasn't as much a crush as an obsession. It's fucking creepy to think that Snape wanted Lily ever since she was nine, and essentially devoted all his life to a dead woman who never loved him back. The scene where he tore apart the photo of the Potters and kept the half with Lily... Just imagine that happening in real life. *shudders*