Toad
Mastermind
Blob
Unus the Untouchable
Mystique
Destiny
Avalanche
Pyro
Vanisher
Sabretooth
Exodus
Black Tom Cassidy
Juggernaut
Lorelei
Others
I'd go for something that alludes to the current groups in the USA, such as Proud Boys and those who raided US Capitol, so I'm thinking:
- Magneto
- Pyro
- Avalanche
- Lady Mastermind
- Blob
- Vanisher
- Rogue
You left out Rogue.
Rogue should be introduced in the MCU as a member of the Brotherhood.
She should drain Carol Danvers and throw her from a bridge.
The first group under Magneto: Mastermind, Toad, Selene (she would be introduced through this manner to give greater credence when the Hellfire Club came around, someone influencing even the outspoken group like the Brotherhood.) They could introduce Spiral or Sauron, as well, perhaps some lower level X-Men villains. Later on they would add Exodus and several other Acolytes after all but Magneto leave or are killed. This group would be focused on mutant superiority but not so much the terrorism that comes with it, though certainly some would be more apt to that than others, so two I would definitely NOT want to see on this: Sabretooth or Omega Red (I leave Selene here as though she's as ruthless as the others, she's also a long game player, not apt to give into her urges like the aforementioned)
There would be a second version though, after Magneto's group no longer goes by The Brotherhood - this would be the iconic version lead by Mystique: Pyro, Avalanche, Blob, Destiny, possibly characters like Black Tom Cassidy and Phantazia as well. While they do believe in mutant superiority, they'd much more likely to cater towards a more terrorist based method of achieving it. At the same time, have Sabretooth or Omega Red in this group would also not feel right. This version would be the more long running version of The Brotherhood in the MCU.
I suppose you could potentially add Juggernaut or Lady Deathstrike to either group, more likely Magneto's though, of course in that case you'd have to change the origins for them to be mutants, which I wouldn't have an issue with.
Fully agree on Selene ,I feel at least initially she should lead the brotherhood, fully cognizant of her own invulnerability as an immortal.She should push for her cohorts to fight for their supremacy over humanity.Later in the film it can be revealed that she was using them as pawns in a classic tale of planning to sacrificing mutantdom for some dark magic stuff basically the Stephen Dorff Deacon Frost move in Blade.Then you have her underlings fracture into the factions you describe- perhaps with Exodus leading one faction and Mesmero/Mastermind another.
One for fun would be.
Sabretooth
Phantazia
Juggernaut
Martinique Wyngarde
Toad
Stacy X
Blob
Depends on who their fighting
Captain Marvel:
Mystique
Destiny
Rogue
Pyro
Blob
Avalanche
X-Men:
Magneto
Toad
Mastermind
Pyro
Northstar
Aurora
(To replace the twins)
I'd just make them a non-Krakoan team of mutants, not villainous team but an anti X-Men of sorts.
Wanda
Pietro
Roulette
Devlor
Ivich
Max Rocker
Vincente
Lightbright
Skein
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Destiny is one of those characters who kinda has to die if she shows up at all. Her power set is just too much of a nightmare for writers that come after whatever comes first .
Mystique should be there but as a side character. Give her breathing room. Much needed. Should also be explicitly evil/anti hero
Juggernsut is obvious
Toad
I could see pyro