GameBoy Advance, like, by far.
Four Swords is the worst thing ever and I wished it actually wasn't even part of the main series. It has nothing that makes a Zelda game a Zelda. Minish Cap is also a pretty disappointing game. Excluding FS and FSA, MC is the worst selling Zelda as well. The DS wins over GBA for me because Spirit Tracks was actually a good game, while the only redeeming factor for the GBA is that it has a port of A Link to the Past. Before the WiiU remaster I found Spirit Tracks to be better than Wind Waker, but WWHD remedies most problems so now considering that version I'd put Wind Waker ahead of Spirit Tracks. Phantom Hourglass was as mediocre as Minish Cap though, so that drags the DS down.
Minish Cap's big problem is that it's ridiculously short for a Zelda game, it's the easiest of all games by far and I don't like the esthetic and the soundtrack. It doesn't fit anywhere with the rest of the games because Capcom just recklessly recycled characters from various games that don't fit together and it's story doesn't take any other game into account. I also find the shrinking mechanic to be pointless, because it doesn't change anything, puzzles as Tiny Link are exactly the same as normal Link.
Yeah, I don't like Minish Cap, I think it's a bad Zelda game.
As far as systems with the best Zelda's go; N64 wins again easily, because it has both the best and one of the best games on it. And even though I think Link's Awakening is the second best game in the series and A Link to the Past is better than Skyward Sword, the GameBoy and Super Nintendo having only one game each puts them lower than Wii which still contains two top entries:
N64 > Wii > GB > SNES > 3DS > GC> NES > DS > GBC > GBA
The games themselves I'd rank:
OoT > LA > TP > MM > ALttP > SS > ALBW > LoZ > WW > ST > AoL > OoA > OoS > PH > MC > FS
