Apparently there was a big old epidemic on the ship that killed off all the smarter castes

Well, all except for Christopher, I guess. He's pretty smart. Or, that lower caste is becoming smarter on its own?

BTW, I got this feeling from The Avengers as well - a lot of the scenes centering around Bruce's... condition, and the powers of Loki's staff felt like they were part of a bigger arc that was mostly cut from the final movie...