As this game IS based on the Second Coming storyline itself--with some Messiah Comples/Wars thrown in for good measure--I feel the endings, for the most part, should be based on epilogue moments from the arc. Which means, that yes, in a couple of endings, Kirt will be dead. Here's some ideas.
The following characters were involved in Second Coming itself (or the previous Messiah stories in Bishop's and Deadpool's case) so the endings would be based on events from the books:
Cable: Basically the canon ending. Cable sacrifices himself and Hope tears Bastion apart. Pretty easy all around.
Cyclops: That bit where he sees more mutants being born at the very, very end. "We were right." I like that.
Emma Frost: Probably her seeing the Phoenix Force awakening in Hope.
Wolverine: "You want a mission and orders? Give them to yourself for once." I hope you know what I'm talking about.
Strom: That last scene with her and Wolverine. "That means this will likely be the last drink we will share."
Nighcrawler: Unfortunately: "In my hour of need...strengthen me..."
Bishop: Maybe not his final defeat per se, but setting up a final battle battle between him and Cable over Hope's survival in the future. Yeah.
Deadpool: One word: CablePool.
Beast: Leaving the X-Men, probably at Kirt's funeral.
Collossus: Swearing to find Illiana in Limbo--probably during the reset-his-arm scene in the epilogue. I like that bit.
Rogue: Getting removed from the combat team.
Xavier: Watches Hope smash Bastion with the comments from the book: "It's like a dream. My dream. The dream. And then its over, and she's a little girl again. Who lost her father.:
Magneto: "I made this asteroid primarily of iron" Cue a lot of dead Nimrods.
Namor: Namor berating Beast for leaving. It's one of his better bits.
Psylocke: "This is X-Force. The only rule: No one knows."
Iceman: Iceman tries to teach Namor Basketball
These characters weren't directly involved to my knowledge, so the endings have a bit more freedom:
Gambit: Continuing from Rogue's ending, Gambit arriving to console her. Some brief mention of his time as a Herald and such, just to show this is them getteng back together after a falling out.
Mystique: A follow up to the Rouge/Gambit storyline. Probably her watching them get back together in disgust.
Juggernaught: Juggs beats Bastion, declares himself "truely unstoppable" and challenges the gathered X-Men then and there.
Omega Red: Collosus vs. Omega Red with Magick's life on the balance, maybe?
Birdy: Joke ending, obviously. I'm thinking something along the lines of some guy at Marvel Comics pitching an ending to the suits where SHE's the true Mutant Messiah, only to get rejected right out.
Quicksilver: I dunno. Maybe something about Quicksilver rejecting Magneto and returning to the Avengers.
Sabretooth: In a snofield in Canada, he battles Wolverine only to get ambushed by X-Force.
Strong Guy: I actually know very little about Strong Guy, but I imagine he'd be a good character to use for a jokey ending.
SECRET CHARACTER: Something involving newspapers and photographs
This is one part of the game development I acutally feel I can help out with. I'll see if I can script out th eendings (I bet I could make 'em short enough) and even do some storyboards. I'm pretty good with line drawing. It's color I have trouble with...
Veterans Day