I would hope one day Alan and Kristy would become a couple. I think if Alan ever truly dropped his defenses and opened up a little (as he tried to in "Stacey's Movie" and the FF's) all of SMS would/should be (even more) apologetic for dismissing him so quickly. Likewise, if Kristy ever allowed herself to honestly "see" Alan, I think, she'd also have a happy (if she'd allow herself to) and shocking surprise. I always saw Alan as a very good-looking guy who was either socially awkward or truly shy. The other possibility is that like Abby, during his earlier years he endured some sort of bad experience or trauma and thus is going the comedian route to cope.
For some reason, I see Alan being persistent (if he develops a crush) and it wears her down and he eventually grows on her. She develops feelings for him but her joking style clashes with his prankster style and in order to make it work they start doing mean little pranks to fellow classmates in order to enjoy each other's company.