would there ever be leaderboards for all of the individual levels in the game, or would that potentially not get used much? (just asking as a primary IL focused runner)

yeah the problem is just that, would anybody use them? no point adding them if they're just gonna collect dust

if you wanna potentially see IL boards in the future, consider making a spreadsheet for this, figure out all the logistics and if there's enough use, it might just happen :)

The Wii version of the level "outta my way" doesn't have all of the enemies. Will my IL speedrun be disqualified because of this?

Also, if I use 2 characters with only me playing both of them, is the IL speedrun disqualified? (Not that I'm actually going to do that, but some clarification would be nice)

You can use any version of the game you like. Using co-op whether by yourself or with others is not allowed for ILs.