Just like the title sounds. Pick a movie, pick an alternate scenario, and have fun!

[hider=X1 & X2] [b][i]I do not support abuse of any kind. I'm just responding to the art.[/i][/b]
So this "What If...?" comes from reading an opinion that Famke Janssen's Jean Grey's character/plot is too wrapped up in the love triangle, when in fact you can remove the love triangle from the movies without affecting much, but you cannot remove Jean Grey without significant changes!  So let's do that: [i]What If Jean Grey wasn't in either movie?[/i]

[b]X1[/b]: The key pivot point here is after Mystique has messed with Cerebro, rendering Xavier catatonic. Not only is Jean the one who finds how to fix Cerebro and does so, but she then makes the choice to use Cerebro which informs them of where Magneto is going. Magneto's plan of which they only [i]just[/i] manage to thwart. So without Jean, they'd have to reason things out. I imagine they'd be able to come to the conclusion Magneto is at the Statue of Liberty, but their delay in doing so would likely mean Magneto's success. 
I mean, they could be just arriving at Liberty Island when Magneto's device is firing up, see it before they land, and fly over to disrupt it from above. But, we know Magneto could just use his powers to move the jet away given he stopped it from crashing in X2.
Ultimately I think we're either dealing with the death of Rogue, or at least the assembly -if not more non-mutants- suffering the fate of the senator: reduced to liquid by Magneto's faulty mutant machine!

[b]X2[/b]: Now, we're not dealing with the death of the X-Men because Jean wouldn't be there to divert the gushing water and lift the jet to safety - the whole reason the dam is busting in the first place is because of Jean's duel with mind-controlled Cyclops. So, that wouldn't happen. Of course Jean not being in the movie wouldn't change the fact Cyclops gets mind controlled, but it would change who's fighting him. It could be Magneto and Mystique, since they're who're with Jean in the movie when Cyclops attacks. Jean actually telekinetically pushes them out of the way of Cyclops' blast, though. But say he is fighting them - Magneto would probably rip out some metal and trap Cyclops similar to how he did on Liberty Island. Cyclops' mind control would cease once Storm freezes Jason Stryker, and they'd just have to return to him and have Wolverine slash him free - no knock down into the boiler room, no destroyed dam. That last bit would be true if Cyclops goes past them and fights the other X-Men. [i]But[/i], if he [i]does[/i] go past Mystique and Magneto, that would imply he's knocked them out of commission, and they'd played important roles in thwarting Stryker in the movie. Plus then there'd still be Cyclops to deal with. Like with X1, I think the delay would be critical - Stryker might succeed.

[i]BUT[/i], actually they wouldn't even get this far because on their way to the dam, Jean is the one who prevented the X-Jet from being blown out of the sky by missiles. Now in the movie she only succeeded in stopping 1 of 2 missiles and they went down anyway, but with far less damage than if both hit. Even if they manage another way to go down with only damage instead of in pieces, Jean is also the one who subsequently assesses that damage and repairs the jet. It could be assumed Storm may know how to perform repairs too - each of the first 3 X-Men (that being Storm, Cyclops and Jean) have been shown capable of piloting, so one could extrapolate Xavier would have them all learn mechanics as well. But in the movie Jean specifically says "it'll take me hours" - time was important, so if Storm had the know-how too, you'd expect that to be reflected in Jean's statement.

So, again, like with Jeanless X1, Jeanless X2 = delay in getting where they need to be in a timely fashion; Stryker [i]will[/i] succeed!
[/hider]

[hider=Last Stand][i]What If Cyclops Doesn't Get Killed?[/i] 
Let's say Phoenix's still intent on killing him, but Jean is able to at first fight against what's going on in her own mind - basically things go as normal up to the point at Alkali Lake when they kiss, then instead of Scott's annihilation, Jean backs off as though overcome by dizziness and/or a headache - they head back to the Mansion together (Xavier could've gotten a sense of things still, or Cyclops calls him, and either way they're going back in the Jet with Storm and Wolverine).
We could still get the scene where Xavier is probing Jean's mind and he explains the mental split that is Phoenix - if memory serves, this was like a psychotic break [i]caused[/i] by Xavier putting up psychic blocks to prevent Jean from accessing her full power? I don't think either Jean herself or Cyclops would be happy with this news. Anyway, things progress and escalate (Phoenix could still kill Xavier and we'd get the "kill me before I kill anyone else" moment; with knowledge that likely the next death would be Cyclops'), and then similar to the Animated Series, Jean decides she can't resist the Phoenix forever.
But here's where we get our next big change - Cyclops would do all he could to figure out another way to stop Phoenix. And the answer is [i]right there[/i] in the original structure of the movie: The Cure! Jean's [i]powers[/i] are taking over. So instead of Magneto getting pumped full of the stuff by the end of the movie, it's Jean. We could still get the Wolverine/Phoenix face-off, but it would be part of a distraction.
And we know Magneto's powers were returning at the end of the movie, so Jean's would, too: this would solve [i]now[/i], but not the future: there's still the aftermath to deal with, and the future to face: this'll happen again when Jean's powers return completely, or perhaps even before. What's to be done?

But that's it for this movie.[/hider]

[hider=Dark Phoenix]Let's have Jean cause more damage at the student party - we see other students' injuries, and say Cyclops breaks a rib or something. I always think Jean's reaction is too overblown for what actually happened - it's not even clear that the power burst was emotion related. What makes it different than any other loss of power control? Like that's what they're at the school for. She just immediately thinks she has to be away from everyone and she's a danger because she knocked people down. The X-Men even treat her like a loose cannon when they confront her - the situation doesn't fit the inciting event, I think. So we'll change that and make the incident bigger. 

Then we get to the main of the What If...? [i]What If Scott finds Jean instead of Telling Xavier?[/i] 
This comes after Jean knocks Scott out. Instead of telling Xavier she's gone and having him find her, Scott manages to find her himself. "What you said to me goes both ways, Jean. I'll always come back to you." I don't really have the whole of this change thought out, I just think it would be an interesting dynamic if Scott's with Jean the whole time rather than "Jean against the world". Perhaps Mystique even doesn't die, because Scott convinces the other X-Men, when they show up, to leave them alone - OR, Scott had told Xavier about Jean's disappearance and Xavier's still the one who figures out where Jean is, but he believes in Scott bringing Jean back and lets him go - come what may. [/hider]

I just realized each of my above [i]'What If...?'[/i] scenarios revolve around either Jean or Cyclops.
[i]Gotta' think of a Nightcrawler one...oo! And Jubilee! My two first favourites.[/i]