We're in uncharted territory for Pokemon. With Brawl and Smash 4, their respective Pokemon games were at the end of development when production began (and both were released a few months after the first public Smash trailer). Designs were finalized, GameFreak already had their marketing strategies planned out. They knew which Pokemon they were gonna push, which they expected would be popular. And the next Pokemon game, in both cases, didn't launch for another two years after Smash came out. Timing wise, it worked out perfectly in Lucario and Greninja's favor.
That's not the case this time. Sun and Moon will be old hat by the time Smash 4 comes out, with the new game right around the corner, but it's likely that even if Sakurai asked GameFreak for a mon from the new games, they wouldn't even have one to give him soon enough. And if Sakurai instead looks back at Sun and Moon to see which mons popular, frankly, I can see him coming to the conclusion that NONE of the Sun/Moon Pokemon need to be in, because none of them have lit the fandom on fire the way Lucario or Greninja did. I actually think it's a bit naive to just assume we'll 100% get a new Pokemon this time around.