X-3 was to the franchise was Ultimatum was to the Ultimate universe. If they are going to continue, it is going to have to be with someone who could breathe fresh life into the franchise and make use of the freedom allocated with the dead/dispatched characters.
-No Magneto
-No Professor X
-No Cyclops
-No Jean Grey
-No Mystique
What they need:
-Sentinels.
It's tragic that one of the most iconic enemies from the franchise was reduced to a thirty second silhouette in a simulation. Since a good deal of the cast has been purged, they will not have to go the 'Days of Future Past' route as they have a roster that could accommodate more development/screentime, and not waste time bringing characters back from the dead. Sure, I was disappointed that the Cyclops and Wolverine relationship did not have a decent arc, but wasting half an hour + of screentime to bring him back is not going to make it better, either. The sentinels do not have to be the major part of the plot, but I would not mind having them engage in the Xmen in one capacity or another.
-Conflict between Wolverine and other Xmen running the school. What I love about the most recent issues of Legacy is the tension and conflicts between Rogue and Wolverine. Whoever ascends to administrator position should contrast against Wolverine.
-Classic Villain: They have a great rogues' gallery to comb through for candidates. I would prefer they stick to mutants, as outside of Magneto, the opposition in the films has been normal people (bigots) and has run its mileage. If they could avoid aliens for the film, that would work. Save them for the sequel.
-Larger battles. First Class set the template for how the battles should be handled,as well as the required scope. Make it outdoors, in daylight, and in an interesting locale. No more government facilities.