Except he is also a game character. Is Tony Stark a comic character? Or is he a movie character?
He's both. Weird how a character can be associated with different mediums at the same time in spite of their origins.
Tony Stark is a comic character. He can be associated with movies as well, because his presence there is quite memorable, and he also has less memorable presence in other types of media such as games. Would that make him a good choice for Smash? No, because he's a comic character.
And Goku has a very pronounced presence in gaming. You can continue to deny fictional characters' duel citizenship in mediums, but the fact remains that Goku has appeared in over 80 video games. In comparison he's appeared in 4 anime, a handful of OVA specials/crossovers, and 19 movies.
He's just as much video game as anime at this point, and denial of that isn't based in logic. It's based in a stubborn desire to classify someone solely by their debit.