Oh I hated Banjo Kazooie. It was annoying that I couldn't run up a hill because I hadn't talked to a mole yet to learn how to do that move.
Mario 64 taught you how to do the moves, but if you learned them on your own you got to use them immediately.
Zelda OoT didn't make you have to learn new moves you got new weapons, and the Gold Skulltas were a bonus side quest. You didn't have to go after them, and most of them you could get in the levels without having to go back half way through the game after getting that last weapon.
Banjoe had some cool things about it, but I think it was ultimately flawed.
Same with Donkey Kong 64. Nice graphics, and the controls were spot on, but the world was uninteresting, and having to play it with 6 characters didn't make it more interesting, but less.
Perhaps I am the only one that felt this way with those games, and if so I will be in the minority.
I will say that I like Nintendo and Miyamoto because he understands that you are still playing a game. He is smart enough to design actual levels and give you noticable visual clues to what exactly your supposed to do in the game. Sure sometimes that simplifies the game, but it also helps you progress and have fun. You in the 3D Mario games you always knew where you were supposed to go. Same with the later Zelda games, and if you forgot you could easily talk to a few key people and they would point you on your way.
Even Metroid Prime gave you hints allowing you to remember where you were supposed to be going.
Remembering that what you are creating is a game is important to the artform, and I believe you will see more and more developers forgetting that imporant task as they create bigger worlds, and giving players more freedom within those worlds.