I say Majora's Mask.
As has been said, most of the aspects relying on 3D can be worked around (for instance, deku flowers and falling off ledges could involve scaling and layers to simulate going higher or lower), and those that can't be worked around can be replaced by something that works in 2D.
If that's too hard (and it very well may be), then my second choice would be Oracle of Seasons.
EDIT: The more I think about it, the more I realize that Majora's Mask might be far too ambitious, a bit pie in the sky.
The game really does rely on its 3 dimensions far more than OoT did. Most of the dungeons use it extensively as the basis for many puzzles, especially Snowhead and Stone Tower (both very reliant on 3 dimensions.
And while I'm sure there are ways to work around those things, it might be more trouble than it's worth, trying to figure out how to simulate the same scenarios those puzzles were built in. I just want this thing to succeed, and I'm not sure MM is that doable.
I could easily be wrong, though. Perhaps they will be easier to figure out than I anticipate, since 2D games have been finding ways to mimic 3-dimensional gameplay since forever...who knows, maybe more of the work is done for us than I realize. After all, even the 2D Zelda games are not truly "top-down", it's more "3-quarter view", allowing multiple tiers and levels to the same room, staircases, etc.
Summary: I really have no clue either way how doable it is, I apparently just like to watch myself type.