Perhaps a mod is in order to make Juggernaut the captured character
I had considered such a thing, but the fact he appears in so many briefing cutscenes made me decide against it for my own mod. I try to make everything feel consistent so my suspension of disbelief isn't shattered. If I had the means of swapping characters in briefings, had access to voice actors, could animate different X-Men/Brotherhood into the cutscenes, then I'd absolutely would have done it by now. If you're going to do it though, I'd suggest making the four items you find in each place his boots, his knuckledusters/gauntlets, his helmet, and then the gem of Cyttorak itself.
I did manage to change at least a tiny bit of textual dialogue in the early part of the game though. I never bought that Mystique and Sabretooth are "cut off" from the team when you have Magneto
right there able to just rip doors off hinges, so I made the silent text read that Mystique had "business" to attend to elsewhere in the facility, then your player character muses about what she might have up her sleeve. My head-canon is there is a weapon there that she wants to lift for herself ó the one Mystique uses that can sap a character's powers away for a time.