He didn't really take over the GSA, he sort of disbanded them and took some members, IIRC.
Season 2 to me is like the best season of Mutant X. We had a better looking Sanctuary, the Ashlocke arc, then some more episodic but still great episodes, and finally a finale that was just awesome. We get to see more character development (just wait until you see the end of "Reality Check", your jaw will probably drop), and the powers just look so much better.
Some of the best Season 2 episodes:
"Time Squared"
"The Future Revealed"
"Understudy"
"Final Judgement"
"One Step Closer"
"Reality Check"
"Lest He Become" (Finale)