They should be in 3D.
Zelda has always been one of the technological showcases for Nintendo. In that sense, as much as I like them for what they were, 2D Zelda is old. And it wouldn't have aged well, unlike 2D Mario.
Don't get me wrong, I love all Zelda games.
I'm glad so many people mentioned Link's Awakening, it's a game underrated mostly. Link's Awakening is a genius game, absolutely brilliant, if there were one handheld game it'd be playing 'til the end of days, that'd be it. The game ranks as my #2 favorite Zelda game, beating out all 3D ones bar one. Also it would be my #4 favorite game in general.
Besides the brilliance that is Link's Awakening, I think overall the 3D games are better. They're usually more rounded, have way better level design, more complicated combat systems and on top of that better stories (again, if Link's Awakening is not counted).
For those interested, here's my personal top all of the Zelda games. Zelda II: Adventure of Link and Four Swords Adventures not included because I've never completed the first and don't even have the second. It shows I don't really care for either release date or 2D/3D, though there are some consistencies to be found. For those a little less familiar, bold is 3D;
1. Ocarina of Time
2. Link's Awakening
3. Twilight Princess
4. Skyward Sword
5. Majora's Mask
6. A Link to the Past
7. Spirit Tracks
8. Wind Waker
9. Legend of Zelda (original)
10. Oracle of Ages
11. Oracle of Seasons
12. Phantom Hourglass
13. The Minish Cap
14. Four Swords








