I figured Apocalypse was the coming big bad just because of how things ended in the old series from '96, but wasn't expecting the Ages arc (assuming that's what's coming).
Everything about this series was masterful. The plot, the characterizations, the voice actors, the art itself. It was a vast improvement over the old series, which was not bad, but this was light years ahead of it. As I said in an earlier post, this blows away nearly all of the films (maybe not Days of Future Past).
Can't wait for the next season. I agree with Sun that Apocalypse will reanimate Gambit as the Horseman of Death, which eventually will bring him back to the world of the living (hope they don't make that too hoaky when it happens). I don't Wolverine is out of the picture because he and Morph are the only two left to deal with Apocalypse in the "present" and that's obviously an issue as suggested by the final scene. Basically, I think we'll have three tales happening over most of the season that will finally converge somehow near the end and leave everyone back in "normal" time.
The studio should do everything possible to keep the same writers around as long as they can!