FFXII's battle system is the first one to come to mind. It did take some time to get used to Darksidesr II's gameplay, but that was only because they completely changed genres on me instead of any particular game mechanic.
Did they? Darksiders 2 seemed like a natural extension of Darksiders 1 to me, mostly.
I feel like I should be able to think of some examples of this, but I am having a hard time right now. Skiing in Tribes games is probably a big one.