Make Cyclops act like Cyclops.
Scott Summers is bad-ass, especially in modern X-comics where he's the leader of mutantkind. James Marsden is also bad-ass and could be an awesome Cyclops if they write him properly.
They tossed poor Cyclops to the side in the first two movies to showcase their poster boy, Wolverine and then "killed" him off in X3: The Last Stand because of his scheduling to do Superman Returns with (the good) X-Men director, Bryan Singer.
Bring Cyclops back the comic book way (he ain't really dead) and let him lead the team for once. Marsden has had a ton of roles in popular movies since X3 and it's time he was handed a prominent role in X-Men. He makes for a much better leader than Halle Berry's Storm.
There's no "I" in X-Men.
By that, I mean there's no "I" in team. The X-Men franchise is strong enough now to no longer need to rely on Hugh Jackman to command half the film's screentime. Have him guest spot or play a secondary character - he's more effective that way - and have the story focus on the team achieving a goal rather then him pursuing his past.
Besides, Jackman will be having his own adventures in Japan come Wolverine 2, he doesn't need a sixth solo flick (I count all four existing X-movies as being his).
Action & Brains
Singer did it all in his first two films, Ratner just brought action into the sequel. Action is useless unless there's some motivation behind it. It has to mean something and make sense to the audience for it to matter, to work, to be cool, and to be memorable.
Remember the big set piece in X3 where Magneto brings his army over on the bridge to fight the defending soldiers and the X-Men? His strategic thinking was to lose two-thirds of his men to enemy gun fire first (they shot anti-mutation ammunition), THEN to have his new Morlock partner, Arclight, take out the weapons? Uhhh... why not do that first, dumbass. I think the 6-year-olds in the theater next to me could of managed that battle better.
Let's not forget the 10 minutes straight of Magneto randomly throwing cars and Pyro lighting them on fire. Ridiculous.
Give us a story that we can get into, a story the characters can be a part of that makes sense.