Greninja was just voted best pokemon in that google poll, I can't imagine it going anywhere any time soon. I could see Pokemon trainer disappearing again and losing Squirtle & Ivysaur since its happened once already and I feel like they only came back because Sakurai was determined to bring back EVERY character.
Incineroar is the most unique of the Pokemon since he's slow AF but tanky and has that whole wrestler moveset motif going for him that no other fighter has right now.
At this point, I Jigglypuff hasn't followed the main cast around in the show for a LONG time, but it
was one of the original 12, so its hard to say whether it'd be dumped or not.
Lucario is also within the top 5 of people's favorite pokemon apparently, so he's not going anywhere either.
Pichu I feel has the highest chance of getting cut. It's pretty much just a slightly smaller, slightly stronger, self-hurting Pikachu. Fun character, don't get me wrong, but if they were ever looking to cut some pokemon, Pichu would probably be the first to get the boot.
They've cut Mewtwo before, but also brought him back in Smash Wii U as DLC due to popular demand and then again for this game. I don't think we'll see Mewtwo leaving in that case either.
If not for Greninja and Lucario placing so high on that poll, I would have said the two of them + Pichu would have been the Pokemon we'd see cut, but at this point, I kinda feel like we'll never decrease in Pokemon at all.
Other than trying to reason which ones have a chance to stay or leave, there's the fact that if honestly consider what the next Smash game will be like, there's an incredibly high chance that a huge amount of 3rd party characters will be cut. I mean, they've already admitted this was tantamount to a miracle and don't see this being possible again. Characters like Sonic or Pac-Man I could see returning easy enough, but they're not going to keep like 40 3rd party companies involved in this. With that in mind, you'd have to think, they won't want the roster to be too much smaller, so they might not drop characters like Pichu at all. I could see them increasing Pokemon, Fire Emblem, and Mario characters even further becuase they'll be losing a pretty fair amount of character slots.