While this point is no longer relevant due to the Disney-Fox merger, I believe that, for the entire lifespan of POP!s, dorbz, Mystery Minis and most of Funko's most popular product lines, Marvel has made a very aggressive effort to make the Avengers Characters the center of attention, rather than the X-Men. While the X-Men are still present and still influence the Marvel Comics Universe, it's definitely the Avengers that have become the "main" heroes. I believe that this was part of a very calculated effort by Marvel that included a decrease in their presence in the the comics, in Marvel animated television and in merchandise (including Funko).
First Funko Product: Captain Rex Wobbler
First POP: Deadpool