Wasn't Yokoi the main mind behind Metroid, not Sakamoto?
Anyway, for me one of the core elements of the Metroid experience is dealing with the world, deciding on routes, exploring and following my own goals (even if the game is designed to nudge me toward the intended goal). Shadow Complex did that very well, Fusion and Prime 3 didn't. The world is the star for me and the background of Metroid I'd want to explore is the world of the Chozo (how they really lived), not the personality of Samus Aran.
Besides, the Metroid Fusion story was pretty much just an Alien Resurrection ripoff.