When it comes to Pokémon popularity, the only data we have with a good potential sample size would be the
Japanese Nintendo Dream one, which had the results go Mimikyu>Primarina>(Dusk) Lycanroc>Incineroar>Decidueye (who didn't place in the Top 14). In terms of other data, the issue is that it comes down to complete hearsay or fan polls, which may not be accurate due to the fact that the fanbase is large and a few online posters may not be indicative of what's truly popular. A good example of that is USUM, which is seemingly divisive among Pokémon fans, but sales would tell you it's close to beating Platinum for the title of second best selling 'third version'. Same thing with Smash since the online community completely missed Bayonetta back with DLC, and Lucario keeps popping up among us as a suggested unpopular Pokémon despite his many promotions across the past three generations within the Pokémon franchise itself. So ultimately, we only have one potentially reliable piece of data to refer to in terms of popularity, the rest could be inaccurate.
With that said, we don't know how much popularity will play a factor in Sakurai's decision as we don't know when he picked the Pokémon and how much it influenced his decision if he even had that information. Theoretically, he could be focusing more on promotion and the concept art, which can go in any of those five's favor depending on which he puts more value on or what he sees in the characters (ex. Decidueye's archery or Incineroar's wrestling abilities).
Even if Sakurai doesn’t care, it’s still possible that The Pokémon Company might care, or that Bandai-Namco might care (since it’s possible that they might be helping with Smash again.)
I doubt Bandai-Namco would care, as mentioned before they shared the other four Smash Pokémon no problem, Greninja being rejected could be due to a number of other factors. Regardless, if Sakurai wanted Decidueye, I don't think Namco would try to stop him, he's still the director and would have more control over the project relative to the company and whoever is sharing work on both projects.
Similarly, I don't think TCPi would be that bothered if both Smash and Pokken picked Decidueye. They have had Pokémon feature prominently across multiple medias and spinoffs within the same generation before such as Lucario, Charizard, and the like, so if Decidueye got the same deal I don't think they'd complain on that front.
True, However Mimikyu is a Team Rocket's main Pokemon of the gen and has Coro pages dedicated to it as well.
Also, Incenaroar is still a very real possibility which has more media presence overall than Lycanroc.
Actually, outside of the movie (which Lycanroc was present in as the rival's secondary), Lycanroc is currently ahead of Incineroar in terms of media presence for the generation. Looking at Bulbapedia, it had the two-shot Pokémon Horizon Manga going into SM, debuted in Corocoro in an exclusive spread shared with no other SM Pokémon, headed a TCG set, was used as an Event Pokémon to sell USUM to early adopters, got a Z-Move in USUM, is Ash's (Current) ace in the anime, was also present as one of Gladion's major Pokémon in the anime as well, also had a lot of merchandise to it, and so on. In general, it's pretty clear that TCPi is trying to push the wolf as much as they can and I would definitely say it's one of the generation's headliners alongside Mimikyu.