Would Wario have been the villain?

If there were a sequel, Mario brothers would be gay dudes imprisoned, and princess would have to save them.

Wario was a brand new villain in 1993 when the first film came out. Although if the sequel came out a few years later, I imagine he hypothetically would been considered for the baddie in the first. Hopefully they'd have a different screenwriter because the first one pretty much had characters that were nothing like their video game counterparts ("Iggy", "Spike", "Big Bertha", etc.)

There was a sequel comic being made a few years back with involvement by Parker Bennett, one of the writers: http://www.smbthecomic.com/

As of last year, it was restarted and it is yet to be finished: https://carlchrappa.wixsite.com/smb2thecomic/comic

I hope this gets completed one day. I have always liked the movie for what it was and seeing people take the time to make a continuation is pretty cool.