Sakurai has clearly stated that this is indeed his last Smash game that he is directing overall (so it is his swansong), he also mentioned that if a new Smash were to be made, not all of the current 3rd party franchises will be brought back, my guesses as to whom might get dropped include:
Snake: Was only added in Brawl mainly to please a close friend of Sakurai's in Hideo Kojima (who is no longer working with Konami) and was likewise only added to Ultimate on the sole condition that Simon Belmont (and his successor Richter) could join (if Snake didn't return, Simon wasn't happening at all), I can see Simon and Richter staying if Konami wants to keep a slice of the Smash cake (and to be fair, Simon and Richter are really all they need anyways), but Snake (who was axed before in 4) is very likely to be dropped again coming next Smash, Simon and Richter have a bigger history with Nintendo, Snake does not (only appearing on 2 NES games, 3 if you count his crossover appearance on that one Gamecube game before his Brawl debut, and 4 is you count the Snake Eater remake on the 3DS).
I can see Mega Man, Ryu and Ken staying put for sure (with Akuma possibly joining as another Echo fighter for Ryu, and possibly Chun Li and Guile), seeing as they have the largest amount of history with Nintendo out of the third party characters combined, so Capcom is definitely staying on board for future Smash Bros games, the same goes for Namco and Pac-Man so long as they stay on as developers going into the next Smash.
Sonic is rather at an iffy spot at the moment (especially when it comes to a 2nd rep, whether it being Shadow, Tails, Eggman or Knuckles), while he's definitely one of the most popular 3rd party characters (he was by far the most requested character for Brawl by a landslide), he's the only third party character that has a perfect attendance (having not been dropped once since he was added in Brawl), Sega themselves are one of the hardest video game companies to strike a contract for regarding Sonic and his series in general (which explains why Sonic has 2 ATs but no 2nd character), Bayonetta on the other hand not so much (seeing as her series have been on Nintendo for all 3 games now (with the first game recently been ported over), I wouldn't be super shocked if Sonic got cut altogether by next Smash, especially if Sega decides to only let Bayonetta be their sole rep (and we all know that Bayo will be getting a 2nd character coming via the 3rd Bayonetta game as DLC, seeing as the game comes out in 2019, which is during the DLC development phase), to make a long post short, Sega is very iffy regarding Sonic, but are more easy-going with Bayonetta.
Depending on what happens with Square Enix's future with Nintendo after the Switch's timespan runs out, Cloud will probably be the first third party character to get cut, seeing as he has the least amount of history with Nintendo and in Smash, FF's universe is the least repped series out of them, with only 1 stage. no assist trophies (where's Tifa or Sephiroth?) and only 2 music tracks to it's name.
Can't really elaborate much on Microsoft, since we don't know if they are one of the companies that is getting DLC or not.