I think the Assist Trophies were chosen and created as a means to homage and advertise the characters and their respective series. Soon after Brawl was released, Sin & Punishment 2 was announced, and what did Nintendo do to promote that? Release it on VC and put a rep in as an AT. What about Little Mac? A lot of people did not know who he was before Brawl, but what was announced at the same time as Sin & Punishment 2? A new Punch-Out! Who knows what they have in store for some of the other AT's (I'm thinking Isaac, Devil, Jill, and Stafy).
Now, within their respective series, K. Rool is obviously more important than Waluigi has, and probably ever will be. I'd rather K. Rool get in over Waluigi any day, but the outcome may be unfavorable.