Just because Shantae is a Spirit and her franchise is kind of already represented in the game because of that, that doesn't mean she is deconfirmed because I believe he is just talking about the roster not everything else in the game.
I think Dukes point was that the statement suggests they wouldn't want to expand on franchises like Pokemon or FE because they would want to use the chance to bring in as many different things as possible.
As for her spirit, it being included doesn't really mean her "world" is included. Adding Shantae would still be music not represented and a stage not represented.
As for the possibility of another pokemon/FE character... If they are interesting and different I wouldn't mind. An FE rep CAN'T use a sword at this point, either get another weapon in there (preferably a staff since an axe would still play like a sword) or use a character who exists outside the triangle. Tiki would be a great option and although she is an assist, young Tiki could still be used. They made a point of showing she will be playable in the Tokyo Mirage port so who knows.
As for a pokemon... There are so many out there that are all so unique. As long as it's not another fire starter and Ideally not bipedal since Ivy and Duck hunt are the only quadrupeds. Also with so many un-reped types it would be nice to get more variety.
If new DLC includes new echos I would suggest taking Smash 4 Charizard and reskinning it as Flygon. turn the fire moves (flare blitz, Flamthrower) into dragon moves (dragon rush, dragon breath) and there you go!