Stealth + Zelda does not work.
Phantom hourglass's running away from the stupid phantoms is the worst thing I've ever done in a zelda game. My hate for the ocean temple was enough to make me not complete the game. I've only done about 4 or 5 dungeons, don't plan on ever finishing it. Also, touchscreen controls and ruined WW graphics made this my least favourite zelda I've ever played.
From what I've heard spirit tracks is more of the same. No thanks.
Wind Waker's stealth segments in the forsaken fortress were annoying, but fortunately not a core part of the gameplay for the rest of the game. They did it once, which was enough.
It's like Nintendo just continuously take the worst parts of their games and make a whole new game around it.
So for the sake of your game/concept, don't do it.