I was under the impression this was a direct result of Wario because of how the costumes were in that game.
Pikachu, Jigglypuff, Lucario, Pokemon Trainer & Sonic all had less costumes than everyone else. Lucario, PT & Sonic didn't require special work, so the excuse doesn't work for them. In fact, the amount of missing costumes between those 5 characters was 6, which is the same amount that Wario gained.
So I don't know if it was true or not, but I always assumed the less costumes for those guys was because Wario took them.
I imagine this game will be better equipped to handle more costumes without sacrificing any, but I guess we'll see.