Here's a good Tumblr post about that very question:
http://marvel-feed.tumblr.com/post/143226578189/who-do-you-think-the-villain-should-be-in-the
They've already had gravitonium on AOS, but Moonstone and Yon-Rhogg would make excelent choices for villains, though I'd rather Marvel sticks with Yon-Rhogg and the Kree. Since her origins are tied to the Kree, it would only make sense for the antagonist of her origin story be a Kree.
They could also use Doctor Minerva. She had some kind of creepy romantic interest in Mar-Vell. Maybe she ends up killing Mar-Vell because she's jealous of Mar-Vell's and Carol's close friendship. She thinks Carol poisoned Mar-Vell against his own kind. This could be a bad idea if not handled correctly, though.
Another idea is using one of the members of The Black Order such as Proxima Midnight. Though, Marvel would probably want to introduce a villain that is unique to Carol.