Stay focused on the good.
Leave SP3 and B&R out of this!!
This is a list of multiple comic book villian movies where it worked because they were careful and kept it simple!
Dick Tracy (pick a villian)
Superman II (Lex's team and Zod's team)
Batman Begins ( Mr. Zzaz, Ras, Scarecrow, Falcone)
Dark Knight ( Joker, Marone, Two-Face, Scarecrow)
Spiderman 2 (Doc Oc, Goblin, Bruce Camebell
)
Daredevil
Hellboy
X Men
Ironman
Incredible Hulk
and on and on . . .
What thes guys need to stay away from is assuming that everyone has to kungfu fight at the end and then blow everything up. Keep the supporting villians on the bench so-to-speak.
if they could stay on track with a story and wrap up/cross each thread as they should, like Dark Knight and SP2 did, then a multi villian/hero story arc CAN work.
Sin City and Punisher did this best. Comic book film writing needs to be on par with these kind of vignettes (sp?).
I remember (sorta) reading the SP3 was to begin with a simple Sandman story, wrapping it up, then moving onto the other two villians. I'm sure that film could stand a fan edit or two.
I do have a fantasy of SP4 starting with Pete waking up from a bad dream, ala Brian Micheal Bendis . .but I bet that won't happen.