It's not just the organic nature of the exploration, it's the fact that Ghost was the first to introduce different stances, with each being effective against different types of enemies. This is just one way and it's off the top of my head. How about using environmental cues, like birds and foxes to find Inari shrines and Haiku mats or hot springs.
Are we forgetting how pristine and immaculate the art was in the game, especially the environment? Ghost almost perfected the AC formula before Ubisoft could and I've no doubt Yotei will go above and beyond even that. Imagine a company like Sucker Punch, who's never made a game like Ghost, almost perfecting a formula that Ubisoft took more than a decade to master and still hasn't figured out how to perfect yet.