I'll bet that in the game once you rescue Catwoman, she'll be all "I didn't need you to save me", and that's the excuse to have a boss fight with her. I'm calling it now people! When that happens, remember Omega predicted it!
Also, for villians who I'd like to see in this. Not including Two-Face or Joker, it's obvious:
Bane. And do it right this time.
Man-Bat, make an excuse for him not flying out of the city, and why he's there in the first place.
Clayface. Try to find him among the large group of minions, and attack him quickly.
Riddler. He plays a big part, putting riddles hinting at something big, and hints about his location.
Scarecrow. More of the same.
Raj/Talia al-Ghul. Makes no sense for either, so just make an excuse for one or both.
Hush. I just like Hush. Great reason, huh? -_-
You know what? I'm just gonna end up listing Batman's entire rouge gallery, from A-List to the completly unknown, so let's end it here.