They add enemies as you progress. Some are immune to frontal attacks, some hurt you if attacked normally and so on. When such enemies are mixed in with a crowd they are a much larger threat, and many of those special enemies can't be countered. Oh, and punching dudes in any of the areas with armed thugs is obviously not going to end well. It's half a stealth game.
The Bamham games honestly get shat on too much here, mostly because people are so used to complain about the industry being shit that some are desperate to bitch about anything. The Bamhams (by which I refer to Asylum and City, the only ones I played) aren't as mindless as people like to claim, due to the many special enemies that get introduced as the game progresses. Another factor is that it's a Batman game, and they managed to come up with a combat system that looks and feels like it suits the character. They could have copied DMC4's combat, but that really doesn't suit Batman.
tl;dr the Bamham combat isn't as shit as people like to claim, it's passable at the least and the enemy types prevent button mashing past the early stages. What sucks is that its combat keeps being copy pasted into games it doesn't belong in. Fucking The Witcher 2 and its randomized attack animations with different timing. Batman combat works for Batman, but I don't want it in my DMC or really anything else.