>>16327089
>Link to the Past -> Ocarina of Time -> Twilight Princess
If you want the same main plot three times in a row with different graphics, then go right ahead.
>I hear Majora's Mask is different from the others
It's only "different" in its emphasis on sidequests, a morbid story tone, and the time-loop gimmick; it's otherwise a direct sequel to OoT, and plays as such. Avoid the 3DS version.
>I also hear Wind Waker is absolute trash
You have been lied to; apart from being (relatively) easy, and some blatant padding near the end, it's one of the series' best.
>Should I play [LttP on Wii VC] or emulate the gba version of Link to the Past+Four Swords?
Unless you have a link cable and multiple copies of the game, just stick to the SNES original; the port's only major gimmick is cross-save item sharing with Four Swords, which requires two or more players to access.
>I've never heard anything about Four Swords
As mentioned >>16316999 here, look for the single-player remake, which Nintendo released for free on the series' 25th anniversary.
>[OoT - N64, Wii VC, or 3DS?]
As >>16329610 says, the 3DS version is the best option; you wouldn't believe how much better the Water Temple is when you don't have to pause and unpause every 30 seconds.
3DS OoT is also one of the only versions to include Master Quest, a kind of 'official ROMhack' that remixes all the items and enemies in the dungeons.
>I just couldn't play an n64 game with a controller with two analog sticks when I'm not even using the second.
The right analog stick is mapped to the four C-Button directions, you nonce.