You know, I agree with you a lot on how B's combat is superior to Arkham's, even if they are different styles of brawlers. But I don't see how Batman's focus on combo and scoring is a detriment or a method of approach comparable to, as you said earlier, speedrunning dodgy NES games or whatever. The main thing to my mind is that it is built around the combo scoring and the leaderboard challenges rather than it is about the challenge clearing the room of obstacles; it's not an extra player-created system layered on top like your theoretical Heavy Rain speedrun would be. It's a deliberately chosen developer-created system. Enemies are resources to be drained of points in the most efficient way possible rather than obstacles to game progression.
That's not to say it doesn't have its problems, the main thing I think is really that combat is so contextual and based on auto-assisting systems that at higher levels of combo play it actually begins to become fairly unreliable in terms of reaction, especially when combo flow relies so heavily on knowing precisely what tool to use next at any given moment and states can change between controller input and monitor output.