I don't see a problem with multiple villains as long as they only focus on one, perhaps two at most and the others are just petty criminals. If they continue the story they can develop those smaller roles later and just establish them in this movie. I think they handled Scarecrow well in the Dark Knight trilogy. He was present in Batman Begins and when you think about it there were 3 villains in that movie and it balanced well because they didn't all have an equal role in the story. You had Raz, as the main antagonist, Scarecrow, and Falconi. If done right I think having that many adversaries can work, but it has to be balanced so that you aren't wasting too much screen time delving into the stories of every single character to a degree that it robs the focus from the protagonist.
I think Batman in general works better as a concept & story when GOTHAM itself is the 'villain'. What I mean by that is, there's CONSTANT crime & corruption that he's always battling against, but never a sign that it's going to get better. It's that struggle against the unyielding enemy of human nature, knowing that it's unwinnable, but continuing to fight against it every night, that makes Batman who he is to me.
In my mind, each of his Rogue's Gallery members is always either in the planning stages of something, or in the midst of it. Penguin is running some underworld thing, Falcone has something going on at the docks, Catwoman is stealing something, & the Joker is just sowing anarchy. That's on top of Gotham just being Gotham. Batman's aware of all of it, but has to prioritize his efforts.
Other than Batman Begins, I'm not sure a film about him has really shown that, & I can't really say how to do it, but I guess I'm just saying that Batman is Batman to me when he almost has TOO MUCH on his plate.