I've mulled over a new X-Men movie for a while and what I'd like to see is this:
Set X4 after the events of The Last Stand and keep that movie in tact.
Cyclops returns to the mansion and we can get a more in depth reveal of the events at Alkali Lake as Scott opened his eyes, Jean stopped the Phoenix personality from shutting down his powers. When a concussive blast hits a telekinetic shield, it would send Scott flying far into the surrounding forest without his glasses. Essentially Scott would have been blind in the wilderness, explaining why it took so long for him to return.
Upon his return, with Jean dead (um...again), let Scott take on the more grizzled "General of an Army" personality from the current comics. His first decision would also be from the comics: Heroes don't wear black leather, it's scaring people. Heroes wear costumes.
You can keep the leather material from the original trilogy, but give it more design and some coloration.
For cast, I'd go with X-Men's 90s era Blue Team with the exception of Beast.
Cyclops
Wolverine
Iceman
Psylocke
Gambit
Rogue
Keep your main group small, develop them well. Wolverine doesn't need time spent on him, he's solid with 4, going on 5, films around him.
For the plot, I'd say after the events on Alcatraz during The Last Stand, the government has seen how dangerous mutants can be. Magneto tore the Golden Gate Bridge and moved it by himself. In response, Project Wide Awake (seen in the files in X2) has been initiated. The Sentinels in the movie would be smaller than the comic counterparts, possibly standing 10 feet tall though we could have a couple of the enormous ones shown in schematics or employed in a single climactic scene.
X4 could be largely a development film with the X-Men building up their work as a team. I'd imagine a danger room sequence more similar to that seen in X-Men issue #1 with Storm (whose role is now headmistress of the school) overseeing it from the control room. On the other hand, we'd see the Sentinels being developed and their first failure would be against Magneto.
Since Psylocke hasn't been introduced before (and I'd ignore the credited name in TLS since she had no resemblance), I'd have Wolverine return from yet another absence at the mansion with Psylocke in tow. She'd be explained as having attempted to kill Wolverine during his trip to Japan, but he vouches for her now (like that'll go over well with Cyclops through the film).
For costumes:
Cyclops: Dark blue with gold or silver trim like the current comics. No head cover
Wolverine: More likely black/gray like his X-Force costume in the comics, also no mask
Iceman: X3...he's ice
Psylocke: Similar to Yuriko's outfit in X2, but no sleeves. Add a dark purple to offset the black on the torso and boots. Rather than exposed skin on her legs, the jumpsuit type outfit contrasts the purple and black. Give her the silver sash of current X-Force and play up her stealth/ninja angle in her design
Gambit: I'd go with his chest piece actually looking like a type of armor, a red rather than pink color, with black pants and knee high armored boots. The classic brown jacket and you've got the classic cajun.
Rogue: She'd need to establish her powers have returned just as Magneto's had at the end of X3. Either the "cure" affected them or she's learned to draw a mutant's powers without harming them and so she can use them for brief periods of time. Her costume would be the basic suit from the previous movies, but give it a green/yellow color scheme.
When the original trilogy was made, Singer was going more realistic in design and that was partially because Hollywood didn't seem sure the comic book costumes would be accepted by movie audiences. Since then we've got Iron Man, Thor, Captain America, and Green Lantern suggesting audiences will accept a more comic book costume if they still have a touch of realism to their design.
I'd end X4 with a climactic battle that leaves the mansion partially destroyed and the X-Men on the run with many students escaping and others captured by the Sentinels (similar to X2 but more violent and devastating to the mansion). Since X4 leads into X5, you simply wrap up with the X-Men defeated but regrouping.
X5 you bring in Charles Xavier (Since Moira is a geneticist, it could be a cloned "shell body" in case Xavier needed to put his own consciousness in. Though he stated it was a man born with no brain function in X3, that could have been just for the lecture's purpose) returning along with Magneto to lead the X-Men in the fight against the Sentinels.
You'd need to establish some way for the Sentinels to begin taking control of America at large, likely with a figure like Bastion assuming control of the program, which would be the X-Men again rescuing humanity as well as fighting for survival.
I wouldn't go all the way to a Days of Future Past story, but you'd certainly have hints of it with some of the imagery of mutants being hunted by sentinels. Beast would cameo, of course, since he's appointed to the UN in X3.
For subplots, I'd focus on Iceman and Rogue's strained relationship with the return of her powers and the smooth talking Gambit forming the love triangle (which felt awkward with Kitty in X3). Wolverine's role would work alongside Psylocke to do the dirty work for the team and Cyclops would be firmly established as the leader. No Wolverine speech to rally the troops, though his past position of influence would make it easy to put him at odds with Cyclops over decisions rather than just over a girl.
Might be a bit rambly and the thoughts might be loosely connected, but it's a few ideas I'd had that I would want to see play out.