I can't speak for Alain's treatment in fanfiction by you or others since it's been a while since I've really read any besides the bigger names like Challenger (one too many badly written betrayed Ash story desensitized me for a while), but at one point there were a lot of stories I saw that had Tobias turned into some sort of one-dimensional villain. I imagine Alain is getting similar treatment these days.
Vilify as in the OOC brand. I don't mind portraying people as wrong or antagonists, but I do object to complete derailings. I read one FF that made Misty into a genocidal loon in league with Team Flare because she disliked the notion of pokemon-human shippings. It doesn't make her seem like an antagonist, but as a means to character shill the protagonist into a bigger Marty Stu.
In other words you don't want to see them turn into soulless abominations that they are not. Yeah, that's hardly an unpopular opinion, at least in the realm of stories and authors I'm a part of. Actually, I don't think I've seen a single...well, at least Amour story, that turns Alain into that kind of individual. But I think most people hate characters being turned OOC for no reason other than "I hate this character".