[Professor S]

I don't really consider Batman Begins to be a multiple villain movie

1) Falcone was a minor character meant to introduce Batmen to Gotham.
2) Rha's Al Ghul was not revealed until the very end.
3) Scarecrow was really the main villian for the majority of the film, and once Ghul was introduced, they pretty much took him out of the main narrative by exposing him to his own chemicals.

I guess the problems come when they split focus on the villains, like they did in Spiderman3 and the later Batman films.