Lately, Sakurai seems to look for Pokemon who he thinks would "fit right in" so to speak. In other words, the Pokemon who would clearly work due to having a design that revolves around some type of fighting. It's not very hard to imagine a ninja in Smash, nor a wrestler, nor a martial artist.
He also looks for Pokemon who are reliably getting promoted by Game Freak, which might be why he's taken a liking to starters recently. The anime is also a strong indicator of which Pokemon could be chosen, as Ivysaur is the only Pokemon thus far that hasn't done anything notable in the anime despite getting in Smash (but even then, Pokemon Trainer is based off the same character as Ash).