Why can you not use 2 controllers in any%? I thought the point of the category was to use whatever is available, so why is the 2 player mode restricted?

There is an any% 2 Controller Category

Yes but why is it a seperate category, and why is it restricted in the normal any% category, the one that most people will see and care about

Because having both categories makes sense. And for Pokémon speedruns we tend to have the most interesting category as the most visible one.

What makes one player more interesting than 2 player? Restricting the 2 player mode is an additional rule, I think that that should be the side category

One player is also the default way of playing the game, so it kinda makes sense for it to be the default category.

Since you don't even seem to do Pokémon speedruns, I think that what the community thinks about this is more important and it's pretty obvious that the community's opinion is that 1 controller runs are the more interesting ones.