Why not make each Act its own individual level rather than each level?

That's a pretty good idea! Done :)

I actually found that separating each level was clearer, instead of separating it in sub-categories in every act ^^ The "Act X Level Y" layout was fine IMO since there aren't that many levels.

Plus the speedrun.com API doesn't make a difference between sub-categories so you would only be able to get the best time from the fastest level in the Act, i.e. Level 1 for the first Act.

I disagree. From a community perspective it makes the runs take longer to optomize, keeping a stable community for a longer time.

Sub-categories in ILs get confusing so I think it is best to make it just Act I, II, etc. without sub-categories or revert the changes.

So you meant the entire Act should be one time? Each level is timed separately in-game so I don't see why that would be better.