I actually think that WW had also dethroned Oot. I had felt that the exploration element was there that Oot was missing. But it also utilized rupies a bit more, also it was annoying how you had to go and catch up to a boat, or wait for it to sail back.. Also TP was better than Oot because there was more things to explore. The boss battles in both games were also really massive(like in other zelda's) utilizing the special item that you had gotten in the dungeon it's self.
So in my opion WW and TP were the two best Zelda games in the sereies.