I just played through all 3.
First I'll just say I loved the story in Origins, however the game world kind of sucks the life out of it to some degree. I don't feel like the Dark Knight protecting Gotham, it's this weird world where criminals are everywhere and you beat the crap out of cops (WTF).
Anyways the combat system in 3 is, well, not as good as the other 2. Everything stated in the OP is true, I instantly had trouble transitioning between 2/3, while the the transition between 1/2 actually felt empowering. I hope they fix this because I really do love the story in Origins.
I just wish the Arkham series were moddable so the modders could do their thing.