Yes agree that the brain should not have been the mastermind behind all. It could have stayed a tool.
For me, the best villain was definitely Raphael
and one of the highlight of the game was when I figured out that I could literally go to hell to rob him and the final fight with him with the song felt so much more epic.
I really enjoyed his lines during the game, and let's be honest: We spend the whole game wanting to kill him and when we can finally do it that's cathartic! That's the definition of a great villain!