Illusio
No words, only rage
I don't know, Charizard, Lucario, Pikachu and Mewtwo are some of the most popular Pokemon. Smash has always put in really popular Pokemon as player characters.
Greninja is the exception as Sakurai has said that the reason he was put in was because he liked what the character could do. That's not to say he isn't popular, but it wasn't the reason for his inclusion in Smash.
Having said that...
Greninja's inclusion in Smash had nothing to do with it's popularity.
Just thought I'd point that out.
Not saying it isn't popular (because it is), it's just Smash isn't a valid example.
While this is true, it should be noted that Smash has a history of popularizing characters and series just by them existing within the game (ex. Fire Emblem being brought over after Melee). So by Greninja being a part of Smash, he's become a lot more recognizable and popular then he already is, and thus is a great Pokemon for them to market.