I don't think it's the number of games that matters, well sort of, but I think it's how much attention Nintendo gives the games/franchise that matters even more. Say, Rhythm Heaven or Daigasso! Band Brothers/Jam with the Band, Rhythm Heaven has fewer games, but it gets so much more attention from Nintendo, so much so that I expect it to get a character before Jam with the Band (which already has an assist anyway, but you get my point, it's not a BIG franchise).
There's a good point there, at least in more current times. Utilising the Pokémon franchise to further strengthen it's promotion, as well as the original usage of naming it 'Tetris Attack' were things done to push it into more focus. Furthermore, as I did previously noted, Lip did herself receive some strong cameos, though almost entirely restricted to Japan (still, that is where Nintendo is based and tend to focus on).
An again, there aren't many of the series left with either much series size nor much attention given them which lack a playable rep in SSB. I guess you could say there's Xenoblade, although that's only been getting much attention with the recent Wii U version. I'm not too sure on how much attention the latest Fossil Fighters or Chibi Robo entries were given, though I feel it was more Japan focused... Nintendo are quite keen on re-releasing Urban Champion... should that count? That said, Clu Clu Land still gets a nice bit of attention with re-releases and appearances in Wario Ware, DK King of Swing, NES Remix and such.
Really, I feel if we also take into account how much focus Nintendo gives them... the only other series I see with fairly decent promotion would be Xenoblade (though entirely thanks to X), Nintendogs, and Art Academy. If we're sticking to retro's though, then the only ones that seem to get a bit of focus to them are the Excite series, Balloon Fight, Urban Champion, and Clu Clu Land.