Hello!

Im new to the game, and can someone explain the difference between versions in this game? (N64 vs ique/wii/wii u). Are there exclusive glitches/strats that only work on n64? Which version is the fastest? I only have the game on wii for now...

Since you're asking about all the versions, I'll go ahead and break them down:

N64: Japanese is faster only for Red Line, Yellow Line, 100% and All Stages. Reasoning for this is because the Carrier boss on Corneria (which is the boss the leads to Sector Y) opens the hatches faster and it saves 4 seconds over the English version. We don't fight this boss in Any% or Blue Line. 

iQue/WiiVC/WiiUVC: iQue and WIIUVC are almost equal speed. These versions remove most of the lag from the game. The bad part about WIIUVC is the input delay, while the iQue version does not present this. The WIIVC version has lag problems on the Lylat map. 

So in short: iQue and WIIUVC are the fastest for this, but good luck getting your hands on an iQue, they're rare and expensive. The JP version is the one you want if you ever plan to run on N64.

All the glitches work on every version of the game, including the 3DS version (which is its own leaderboard). The only 'glitch' in the game is the Katina 4 hatch trick, I put it in quotes because it's pretty hard to say if it's really a glitch. The hatches are present inside the mothership, but are not meant to open until the cutscene plays. Destroying the 4 hatches spawns the core early, allowing us to cutscene skip, saving over 30-40 seconds.

No difference in glitches, but the gameplay style is entirely different on N64 versus Wii/WiiU/iQue due to lag. The N64 lags a lot and we do a lot to reduce it as much as possible. The other versions don't, and since the gameplay is pretty fundamentally different the boards are split. 

Fastest to slowest versions are as follows:

Wii U
iQue
Wii
N64 (JP is 4s faster than US for Corneria's Attack Carrier boss only)
N64 (PAL)

Thank you guys so much for fast and detailed answers! Im gonna pick upp this game for sure... shame that the iQue is so unreachable unless you got a deep wallet....

@30cents: so the jp n64 version is faster for those categories... does this 4 second timesave also work on jp wii version? Or is the jp version on wii even a thing?

The 4 second time save can also be on Wii, correct!

Do not bother with the WiiU version either, no matter what controller you use to play it the game will have significant input lag when shooting.  Basically its so major that you cant mash or tap out enough shots to kill a boss fast.  Ive gone through the trouble of testing this myself on WiiU using mutiple controllers.  Like everyone else said if you can manage to get an iQue player, its probably the best version basically due to the controller being similar to an N64 as well as the input when firing shots.

only downside is its expensive, but you would only be ever be challenged by others who own one.

Unless someone can prove me wrong, the Titania audio cue glitch doesn't work on the Switch version. I tried it earlier with the setup successfully but boss music still played.

I got 2 things to say about this...

"it's pretty hard to say if it's really a glitch" when referring to mothership skip is just foolish. You do glitch out the game as it completely messes with the flags and the cutscene gets destroyed and will never start once you pop the hatches. 

"The JP version is the one you want if you ever plan to run on N64." really is ignoring the facts started before saying it. Clearly for N64 gameplay on Any% or Blue Line, this is not the case.