Well really I think that a 3D model is a good idea, even if you are using sprites. Make a reasonable 3D model of your character and animate him, then render it as sprites. You could of course manually edit after rendering to neaten things up, render at double the resolution you need, then rescale to get nice AA around the edges.
I dread animating 2D stuff. 3D objects in a 2D game is certainly a good option for DBPro too, I do that quite a lot in my projects, remake old 2D games in 2.5D, using models and 3D meshes, but in a 2D environment coordinates wise. With a zelda game, I personally would be tempted to go for a DS style, like the DS version of Zelda, traditional top down 2D game, but with 3D visuals. Link looks good in low poly 3D.
What would concern me is quality, most people can't draw good 2D tilesets, it's a real skill - although I don't know how your skills are, I can only go with my own thoughts, and for me, 2.5D is the only way. There are a lot of overheads in 2D with a zelda game, like Z-depth sorting, which can really drag things down. With 3D, there are less concerns, it's quicker to create the media, the media works better, you won't have to work like a dog just to get a basic scene together. I guess it's similar to Animal Crossing DS as well, that works really well too.
I would go for a 3D environment with 3D characters and 2D sprites, with a fixed camera you can use flat plains as sprites. So really you get the best of both worlds I think:
See the characters and level are 3D objects, low poly - but those bushes, collectables, those are 2D plains. With that, you get an inviting game, it's accessible and quick - just looking at that you know that you can run around slashing up bushes and grabbing diamonds, no clunky collision detection or complex controls. It just makes sense IMO - 2D bushes means they can have leaf particles flying around if you want, collectables can shimmer or shine or whatever you like - all fairly difficult to replicate in 3D. If I was making a top down RPG style game, that's what I'd go for without thinking twice - best of both all the way.