Thats very interesting, I didnt actually know that but I figured a majority of the plates would be under the ocean 
I know where you are coming from with the Civ settings, Ive played those games to death since the first one and typically choose my own settings so I know how limiting they really are, especially in regard to the age setting. I think your ideas are certainly an improvement on that formula even if its complex, one thing that crossed my mind is cloud cover especially on the topic of mountains, that if you have disasters like tornados and whatnot it might be cool to have just regular weather cycles which cause rivers to fill up or dry out so the world actually ages with you as well unlike the Civ games 