In my opinion, there is no strongest faction; they are all equal (that's what balance is for). Personally, I don't know how to play, and I don't want to learn how to play, as Tower, Stronghold, and Dungeon. I also don't play Academy very well. And therefore, for me personally, the two strongest factions are Necropolis and Haven. But! I repeat once again, this is only because of my preferences and skills, and nothing more, and there is no faction that is stronger than the others.
Maybe you're right, but I'm still all for Stronghold and Necropolis....