Assassin's creed 2. In the first game, grabbing would result in Altair grabbing the enemy by the collar, and almost immediately hurling them in what ever direction you flipped the analog in. In addition, enemies could do the same thing to you, making the combat feel real and organic.
In the sequel, the grab mechanic is replaced with a grab and hold, which allows ezio to hold on to an enemy for an extended period of time and slit the throat with a button press. This time around, enemies couldn't do the same. This change had 2 effects: Scaffolding and merchant stands became obsolete (whereas in the first game they were fun and rewarding to use), and enemies became less aggressive, ruining combat for the game. It sounds like a small change, but it really made a huge difference.
Don't get me started on brotherhood.
Another prime example is F.E.A.R. 2.
It made 2 mistakes, one of which was exclusive to consoles.
It's first fault was that it made me use the bottom triggers to shoot (I had it for ps3...yeah.).
The second problem was that there was too much combat. The first game made outstanding use of suspense and paranoia, but I never felt that in F.E.A.R. 2 because I spent all my time shooting. And honestly, the shooting wasn't even as awesome as in the first game.