See, I think I have probably listed every game except Four Swords Adventures of the type of Zelda game which I have not played. :-p

There's NES LoZ, which is basic overhead. There's AoL, which is side-scrolling (mostly). Then there's the more advanced overhead of ALttP, which (from what I've seen) has better graphics, animation, movement and flexibility. I think every original handheld game (i.e. not NES Classics, but obviously still including the GBA ALttP) has based itself on the general structure of ALttP, presumably because it worked so well. (That would seem to point towards ALttP GBA being the best option. I do have a SNES, but it's so crappy I might as well not have.)

If I were to continue on, I would then say there's the 3D of Ocarina of Time and Majora's Mask, the advanced versions of that seen in The Wind Waker and Twilight Princess, and whatever Phantom Hourglass is supposed to be.