I liked some of things already stated in the thread. I'll pick another element to expand the discussion.
Ideas liked so far: Apocalypse angle would have good to touch, especially with 2 of the four horse on the team and leading.
Gambit/Polaris pairing. I would have wanted that developed. Whether it lasts or not isn't the issue. It's coming together with some commonalities and attraction that do exist. For the record, this view has NOTHING to do with Magneto, revenge or Rogue. In fact I could care less about those things. It has always been about exploring a relationship that isn't the same old stuff. There is nothing to read between lines for because there is nothing between them.
The Thieves Guild being dropped like it was the plague was bothersome. And I also liked the idea of corp espionage by Gambit.
Now, let me see. I think with the build up of suspicion of Quicksilver - more could have been done there to the point of being caught talking to Havok. A confrontation and maybe an ultimatum to talk to Polaris that sort of thing. In the end, I would want some sort of truce and working on trust between Gambit and Quicksilver.
Would have never used the Georgia storyline. Not when you have Polaris, Gambit and Quicksilver with all of their history. It was a waste and short changed fans of a better story with the main three.
The other ideas in this thread could have easily been a storyline instead of Georgia's.
I think the biggest disappointment is how PAD handled things.