Alexander Hutchinson, the creative director at Ubisoft Montreal has confirmed that for Assassin’s Creed 3, they “rebuilt the combat system from the ground up”, and:
Everything from the player strategy, to enemy types, to animations and camera implementation is new. Connor’s combat system is based around a two handed fighting style, so he uses either tomahawk and knife, assassin’s blade and knife, as well as many other combinations.
There’s also talk of the redesigned health system. So, “instead of having health units and needing to heal after combat, you now have a regenerating health system which means you can’t regain health during combat – you need to escape and rest. This exponentially increases the challenge.”