For a season 2, I'd love to see Bastion and an Operation: Zero Tolerance style storyline somewhere down the road. They could even keep Wolverine as a focus, but it'd be badass if they had Wolvie, Iceman, Cecelia Reyes, and Marrow fighting the sentinels alone while the rest of the team gets kidnapped or something.
Or, stick to the 616 story and have Wolvie, Cyke, Jean (if she comes back and stays), and Storm rescuing a kidnapped mutant (Jubilee), while the subplot could be Iceman, Marrow, and Cecelia. You could throw in Beast with the Wolvie crowd for good measure, and maybe Kitty or Nightcrawler with Iceman. Angel and the others could be kidnapped or just not part of the story.