The whole idea behind the Zelda series is of exploration and having an open world. Sure, you can warp everywhere for convenience, but the game rewards you for walking or riding places by giving you heart pieces or bugs or other such things. So I'd have to say no to a more linear world.
I don't, however, mind the idea of a different progression of the storyline. I can always expect a slight plot twist after three dungeons and then get the Master Sword. Twilight Princess got knocked in a few reviews because of this.
So, basically, I wouldn't mind a few more twists and turns in the plot. I also wouldn't mind a little more mixing up of the missions - the escort mission and the saving of Colin in TP were on the right track, and I wouldn't be surprised to see group combat with larger numbers of enemies in a new Zelda game.
Speaking of combat, I loved the unlocking of new sword skills (the Stalfos teacher dude was just awesome) and I would like to see combat in Zelda expanded a bit more. Wind Waker introduced ideas that TP expanded on, and I'd like to see combat evolve a bit more.
Unfortunately, given Nintendo's ridiculous production cycles we probably won't see another Zelda game 'til the next console.
Wow, this was a really long post. My bad.