I know, I find that weird about Bobby being homophobic - I mean he didn't treat Jean Paul any differently in the comics after Annie called it him. Maybe Carey meant instead of homophobic is that Bobby probably is bi but just isn't that comfortable with exploring it? I mean from his reaction from getting a secondary mutation it'd be understandable. If he was scared of standing out as a mutant because he looked different it wouldn't be a huge leap to imagine him being scared of standing out by admitting he's bisexual or dating/sleeping with another man.

A JP POV fic would be good, exploring his reactions and feelings whilst also keeping the mystery and having the reader go through the same train of thought with him but since you've already started this one in a different way it would be a shame to change it. I'm sure you could think of another fic to write where you could have it from his POV only, like a post Hand brainwashing storyline.

Hehehe, anyway I'm sure wherever you decide taking the story will be great and if its still a tough choice you could always have alternate endings? Then you can make one the main and the other the 'What if?' like Marvel does all the time, lol. :)