Alan is Sanguine's champion.Self-explanatory; Alan was given the drugs responsible for both movies as gifts from the Daedric Prince of Debauchery. And considering Sanguine's actions in Skyrim...
The third film will lampshade a lot of the series' tropes.For example, at the climax, someone, probably Alan, will tell Stu that "now is usually when you figure everything out".
Chow will die in the third movie.And his final words will be "Toodaloo, mothafuckaaaaaa...!" or "...so long...gay boys..." Jossed: It looks like he's going to die in one scene, but it ends up being averted.
Every time Stu is having a shitty day, he sings an improvised song about it.He demonstrates proficiency singing and playing instruments, and both times his friends don't see anything amiss at him breaking into song. I think Stu has been doing this since he was very young, so often that his friends became used to it ages ago.
Chow Invites himself to Alan's WeddingAnd even after realising Chow is a proper murderous villain Alan goes along with it for old times' sake.
Alan has AspergerSyndrome.Between the social awkwardness, the childlike demeanor and the insane amount of skill in a field (in this case, math), it wouldn't be out of the question to say that he may have it.