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What he means, most likely, is that all these 3rd-party characters were given special permission to be in this game, and Sakurai is not certain he can get that special permission again. We saw it happen with Snake for Super Smash Bros. Wii U/3DS, in that he didn't return because they didn't receive said permission.
Typically, what happens in licensing is that if something proves to be a success, the licensor will demand more money and more control the next time around. (And there is no doubt SSBU is a success, as has all of the DLC.) That can be negotiated, especially if one can convince the licensors that they would be unable to turn a profit or it would severely decrease the quality of the finished product. SSBU is vulnerable to this because the legal team works with so many other companies, not all of which get along and may demand things that are mutually exclusive with something else.
This is a major reason why SEGA ditched the crossover angle for Sumo Digital's racing games and stuck strictly with Sonic, for instance. Each franchise creator has some say over how their characters and environments should be like, and whether or not they get to be in the game. This is reasonable, but it does dramatically slow development at times. Ulala (protagonist of Space Channel 5) spent a long time in development for Sonic & SEGA All-Stars Racing, for instance, because the creator is a perfectionist and kept rejecting Sumo's 3-D models for her approval. Toejam & Earl were planned to be in Sonic & All-Stars Racing Transformed, but the creators refused, saying they'd rather have Toejam & Earl as DLC if the game proved to sell well enough for them, which apparently it didn't. I forget who it was, but another character had to be removed from the roster when they discovered the game was to be on the Wii U. Their contract stated that the character would be allowed only if the game's Wii U development was canceled; they decided they'd nix this character so they could release the game on the Wii U.
No doubt there are a LOT of legal requirements Sakurai is not telling us about SSBU, especially Pokémon characterts and third-party characters. Suspect are the extremely small track list for Midgar and the complete lack of in-house remixes for Sonic music.