There really isn't such a thing as a character or series "deserving" more reps, in my opinion. Also, I really, really think we all overanalyze the heck out of how characters are chosen. I do not believe they are chosen because "X series needs more characters" or "X character deserves it for X reason", I believe it simply comes down to what Nintendo wants to market at the time mixed with Sakurai's vision for each individual game. For this game, he wanted to make a big crowd pleaser, which is why the main gimmick was "Everyone is here!" and having some of the newcomers be hardcore fandom picks like Ridley and K. Rool. Another thing that I think isn't the best mindset to have is thinking every character from K. Rool onwards is gonna be a hardcore Smash fan pick. Yes, Sakurai has said he went to the ballot for ideas, but that's the main thing: Ideas. He did not say that every character was going to be a core fandom pick, nor did he say they were all coming from the ballot.
If Pokemon got two characters, it's because Nintendo will of course market and push what is most likely their most profitable franchise. Heck, it's pretty dang clear (IMO) by the way FE characters were chosen that they were most likely crammed in as much as they were because they wanted to ride off of the hype Awakening caused. Pokemon is having a huge resurgence right now and is bigger than ever, so yeah, I don't think it's too far fetched (heh) to expect this game to give us more than Incineroar, whether it be from base game or DLC. Would it be nice to see characters from other series? Yes, but they aren't going to get put in the game because of reasons A, B, and C, they'll get in if it's what Nintendo wants. Sakurai has the power to choose newcomers, yes, but Nintendo has the power to say yes or no, and what they want is what they're gonna get. If they want more Zelda characters in Smash? They'll put more in. If they don't? Then they won't. Simple as that, IMO.