WBGhiro: Even though it got some hate I think i'll stick with TP, I'll try the wii version since the HD port seems to just have some kind of grey filter slapped on (Or is it just me?).
The Wii version is definitely the worst. The motion controls were shoehorned in at the last second as it was developed as a Gamecube game but then ported to the Wii as a launch title. Unfortunately the motion controls are obligatory in the Wii version. There's a reason the Wii U version reverts to the GC version's controls and doesn't even have an option for 'waggle' despite the Wii U supporting Wiimotes.
Just in case you think I'm simply opposed to motion controls, I thought the next game (Skyward Sword) had excellent motion controls. I don't hate motion controls in general, but Twilight Princess's motion controls were pointless and awful.
The Wii U version also undoes the mirroring that was applied to the Wii version. They wanted to make Link right handed for the Wii version after developing the entire game for the Gamecube with him left handed and decided the best (cheapest) way to do so was to mirror the entire game.
So... unless you have a Gamecube and the opportunity to buy the GC version I would recommend the Wii U version for the controls alone.
WBGhiro: I've got a 3DS XL, is there a NEW new one or did you mean just the new one?
There are two generations of 3DS systems:
1: 3DS, 3DS XL and 2DS
2: New 3DS, New 3DS XL
The second generation systems are more powerful and there are a few games that only work on them and some that just run better and make use of the C-stick and extra buttons. SNES games are available on the 3DS eShop, but only for New 3DS (/XL) because it requires the additional processing power. This will be why Elmofongo was asking.