One of the things I disliked in Shake Dimension was that instead of using traditional doorways, Good-Feel opted for Mario Bros-style green pipes all throughout the game.
I'm fine with pipes in Wario Land games, but they shouldn't replace doorways, and they should not look like they've been ripped directly out of a Mario game...
Warp pipes for actual warping and doorways for just going into another area.
As for what CM30 said, BotW needed that kind of warp because the world is just ginormous. But this game would never be that big.
I mean, Metroid itself really doesn't allow you to instantly warp anywhere at any given time.