Given this is Nintendo we're talking about, and how protective they are of their own characters, I wouldn't be surprised if the movie contracts heavily favored them. I feel like they'd add some provision in there that they can still use their own characters in different media or projects, maybe just altering their designs a bit to keep things distinct between projects. So, I think some form of Link could still show up, despite the live-action movie. It's possible that live-action Link can't show up in Illumination Mario movies. But, a Link based on Tears of the Kingdom or A Link to the Past Link likely still could. Maybe. I don't know.
Characters outside of the ones Nintendo owns? Those are less likely. Pikachu makes more sense than Sonic.
I will admit, the more companies that get involved, the less likely this becomes. It's hard enough to negotiate a crossover between just two companies. Never mind, 4 or 8. But...I can't help but think Nintendo knows how popular Smash Bros is, and would have been thinking ahead about how to make a Smash Bros movie happen. Especially since Marvel and the Avengers made shared universes so popular.
So, I'm not holding my breath for this or anything. But, if it DOES happen...I reserve the right to tell you all "I told you so".
But, just for the sake of argument, what else COULD they do for a Super Mario Bros 3 Movie?
Because, like I said, they seem to be using a LOT of stuff from almost every game in the series in this one. It seems like Galaxy is going to be about hopping from planet to planet to visit these different worlds from all over the Mario canon. That's how we're getting stuff from American 2, World, and Odyssey in here. And we even have Bowser Jr, which means we have elements from Sunshine or Wonder, too. I wouldn't even be surprised if we do get some Land/Gameboy love in there, if Daisy shows up. I could see Luigi getting a meet-cute with Daisy, while they're in the middle of world-hopping.
So, what does that leave us for the third one?
Well, the Koopalings are the most obvious characters they haven't added in, yet. And, yeah, having them be in the third movie makes sense. But, I'm not sure they're "main villain" material? They could be, but I'm just not sure. They're better henchmen than main characters, in my mind.
We kind of already got Mario Kart in the first movie. But, we haven't gotten all the Sports or Party games in there. Maybe they could do something with everyone being forced to play a cursed board game, like Jumanji? That feels like it'd be lower stakes after Galaxy. But, it would make for a pretty fun movie.
Zamuel makes a good point about bringing in stuff from the RPGs. And just a shot of Exor the Giant Sword coming down from the sky would be a pretty great teaser image. And maybe we could get a "Legion of Doom" type thing with all the RPG villains teaming up? Exor or Smithy from RPG, King Olly the Origami King, Dimentio or Count Bleck from Super Paper Mario, Grodus or the Shadow Queen from Thousand Year Door, and of course Fawful from Mario and Luigi. That would be AMAZING! And it'd give us a excuse for Mario and Bowser to team up in the final movie. But, also...it's maybe too deep of a cut for casual audiences? I'm all for it, but I don't think it'd be very likely, unfortunately. At the very least, it feels like Miyamoto doesn't care for the RPG side of the franchise, so I don't think he'd let the third movie go in that direction.
Wario is another good choice. But, if we do that...I have to wonder if we'd be in for a "multiverse" movie? Wario isn't from a alternate universe in the main games, but I can see the temptation to turn him into a mirror-verse doppelganger of Mario. So, maybe Wario shows up, and Mario has to form a team of other Marios from other universes to take him down. Paper Mario, Super Show cartoon Mario, black-and-white manga Mario, theme park mascot-suit Mario, breakfast cereal mascot Mario, original pixel-art Mario, etc. The Multiverse of Marios! Something like Mario and Luigi Paper Jam, but on a MUCH larger scale. That way we can still get a big team-up, but we don't have to go outside of the Mario franchise in order to do it. I know a lot of people are tired of the multiverse, but, personally, I still dig it. I think it'd be a fun way to escalate things.
So, personally, I think if we don't go full Smash Bros for the third movie, I think Wario makes the most sense as the main villain. Maybe Wario teams up with the Koopalings. Which...is something I don't think we've ever seen before? But, if we lean into the whole "multiverse" idea, maybe the Koopalings come from a dimension where Bowser and Peach actually became a couple? That'd be...a twist, alright. That probably wouldn't happen, but it popped into my head, so now I must put it into all of yours!
That's the best I can come up with. Anyone have anything better?