Personally, if I were to give a general setup for X4 I'd do this:
-Bring Back Cykes: No Body = Can't be sure he's dead. I thought of the idea of him being knocked back into the woods after Jean went crazy, and he's found my Emma Frost..which brings me to next idea
-Introduce Emma & The Hellfire Club: Introduce The Hellfire Club a group of wealthy entrepenuers that are paying to back Senator Trask's Sentinel project. Still trying to piece together what their reasons for backing Trask would be. Members would include: Sebastian Shaw, Selene, Mastermind, and Gambit.
-Introduce Trask & the Sentinel Project: After the events of TLS stand, setup Trask is vehemently trying to pass the new Sentinel project to help detain what he calls "dangerous mutants", when in reality he means all of them. Don't make the Sentinels the huge 20 story robots. Make them about 12-15 feet high.
-Emma & Cykes: Emma using her telephatic powers has Cykes brainwashed into joining the HFC and ultimately becoming their White King much to the dismay of Shaw. Emma and the HFC use Cykes to exploit the X-Men's weaknessess as they go against the Project Wideawake.
-Gambit: Gambit isn't really a full fledged member of the HFC. He's just basically their bodyguard who begins to form an affinity for Rogue during the X-Men's numerous encounters with the HFC. Eventually turns against the HFC towards the end.
-Rogue & her powers: Have Rogue gradually start to get her powers back throughout he movie causing her to once again relive the pain she felt when she first manifested them. The strain of this situation takes it's toll on her and Bobby's relationship and they finally put an end to it. At the end, with the help of Gambit, she finds the strength she always lacked in her powers and really finds herself.
-The X-Men Team: Bring back Wolvie, Storm, & Beast and the elder/leaders with younger crew of Iceman, Kitty, Rogue, & Colossus. Bring in the new crew of Jubliee, Siryn, & Sunspot.
-Magneto: Not the main villain this time. Give him time out from the battle this go round.
That's the general direction I would take it.