almost no one plays on VC because these versions are bad due to all reasons you listed.

99% of the people played on N64 with N64 controllers.

there was one person who got high enough using Wii VC. hopefully they can respond if they're still around.

^That'd be me I guess. Haven't been able to respond for a little while but I'm still around, though I usually keep more of an eye on the discord than the fourms these days (not that I actually talk often ).

I used to use a GC controller but yeah the triggers are terrible for DTs/DTDs. I don't remember how good/bad the stick was but the squishy triggers were bad enough for me to get a classic controller.
iirc there was another top player who played on Wii VC and used a GC controller, though I don't know if they swapped controllers and/or platforms at any point.
My first controller for this game was actually some random 3rd party controller, but the less said about that, the better.

I've stuck with the classic controller for over 10 years now, partially because there aren't many different controllers to choose from, partially because I don't want to buy an N64 + accessories just for this game, but mostly because I don't have any major issues with the classic controller especially compared to the GC controller so I never really felt the need to swap controllers again.
The shoulder buttons on the classic controller are a bit soft and the analog stick could definitely be better but those are minor/non-issues for me...but that might have more to do with me being used to the controller rather than the controller itself being good.

Also, I'll admit that I was completely oblivious to how bad the Wii VC version is compared to the N64 version for my first few years of playing. By the time I heard about all of this from the other players, I was already in the top 10. Go figure.
For real though, playing in PAL is probably a bigger issue for me than playing on Wii VC due to how much easier it is to mess up the DT rhythm compared to NTSC.

i can see the classic being better than a GC controller because of the triggers. those help a lot.

also, yeah it's true someone can get used to those controller's sticks if they play enough or start with them to begin with.