The reason I'm not particular a fan of Nintendo vs a company is mainly because even with a decent size roster for each company, I feel Smash Bros. has such an impact that you can't expect the Nintendo side to have anybody that isn't already in Smash Bros. Despite how quite a bunch of people want to have lesser known Nintendo IPs for a Nintendo Vs Company, Nintendo's biggest advantage is also it's biggest weakness is that there are so many must-haves that you'd have hardly any space for characters that would be new.
- Let's do a hypothetical roster for Nintendo vs Company with 25 characters each. So first off, we start with the Mario series and so easily, the must-haves are Mario, Luigi, Peach and Bowser. Already that's 4 characters.
- Next are the series connected to Mario, so next up would be Donkey Kong, Yoshi and Wario. So already that's another 3 for 7 characters.
- Next up is the Legend of Zelda and obviously the Triforce. Link, Zelda and Ganondorf are all important, so that's another 3. We have 10 Nintendo characters.
- Pokemon and Animal Crossing would be next on the list, but we're going to save them for another topic for reasons I will discuss later. For now, we're skipping them. So after the big 5 of Nintendo, we can go into Nintendo's lesser, but still big series and icons. So next on the list would be Metroid, Kirby and Fire Emblem. Samus and Kirby are absolutely Nintendo icons and with Fire Emblem becoming big, the easiest option is Marth who has become a prominent character and one of the faces of Fire Emblem, so Samus, Kirby and Marth are there. We have 13 Nintendo characters.
- After these 3, Splatoon is definitely in the running, with it being an incredibly popular series since it's first title and the Inklings themselves have become notable Nintendo characters. And the easiest answer are the Inklings and they also have the benefit of having the code names, like "Agent 3" and whatnot. That said, they'll most likely add in the female Inkling if they can't do the Smash thing where you can choose between the male or female, since Monster Hunter in MvC Infinite was exclusively female. So we'll add them to the roster for 14 characters.
- After Splatoon would be Xenoblade. Xenoblade has become a notable Nintendo game series which got it's much needed start with Operation Rainfall encouraging Nintendo to bring it to the West and then getting a massive boost in popularity with Xenoblade 2 and 3. The real question is whether they will do Shulk or Rex with Pyra and Mythra as back-ups. But regardless of which one they add, that would be another character for a total of 15.
- Now we start heading into the lesser franchises that still have notably popular characters. Fox and Pit are easily the biggest in terms of lesser franchises with big hits. Captain Falcon himself, despite his series being not big, is easily a big cult icon because of his popularity in Smash Bros. And Smash Bros. would have just as much impact on a Nintendo vs Company game as it does in gaming. So those 3 I have no uncertainty of them getting in, so we bring up our list to 18 characters.
- We will now talk about Pokemon and Animal Crossing. The reason why I wanted to talk about these near the end is because they have some notable issues, but would have a big impact on the roster if handled. Isabelle would be picked since she has since become the series mascot. Now her and Animal Crossing's issues are:
- Whether they or not they would have a moveset in mind for her
- Whether they do want to add her in. If they want to add her in and do give her a moveset, we reach 19 Nintendo characters.
- In regards to Pokemon, the big issue is whether or not they have cooperation with Gamefreak and the Pokemon Company in wanting to add in Pokemon characters. It's a non-issue with Smash Bros. at this point, but whether they want to allow Pokemon to go into another crossover fighter would be another story. And quite easily, the biggest names for Pokemon would be Pikachu, Mewtwo, Lucario and Charizard. Pikachu, Mewtwo and Lucario would be shoe-ins, no doubt in my mind. It's really Charizard who they could potentially skip with the potential Pokemon Starter of the month and to not flood the Pokemon characters with Gen 1 Pokemon. But if Pokemon were to get in, much like Mario, I would see 4 reps getting in.
That would be 23 Nintendo characters, with only enough room for 2 Nintendo characters left. I am absolutely certain the 23 characters above would get in without hesitation which really only leaves 2 Nintendo characters they need to choose. And the biggest thing to note is that aside from Mario, Zelda and Pokemon, none of the other franchises that are also in have a 2nd character.
And no matter how much people want there to be a series not in Smash to appear, why would Nintendo choose 2 lesser known games or series to get a character over an additional character for 2 franchises without a 2nd character? I can easily see another Kirby character, another Fire Emblem character, another Splatoon character, even Ridley I can see getting in over a new franchise not in Smash Bros.
We didn't even talk about the franchises in Smash that haven't entered yet, like Punch Out, Earthbound, ARMS and Pikmin, not to mention Ice Climbers, R.O.B., Wii Fit Trainer, Mr. Game & Watch and Duck Hunt. Even if we didn't get Pokemon or Animal Crossing, I can see these characters getting in and these series getting a character in alongside the additional characters for franchises with only 1 character over a new franchise/game that didn't have a playable character in Smash Bros.
This is easily my biggest issue with a Nintendo vs Company game. The amount of Must-haves that Nintendo has alongside the impact that Smash Bros has had on it's characters and it's audience. They have so many characters that are so recognisable that they can't not put them in and if they have space for characters after them, they would pick the characters that people would easily recognise from Smash Bros. rather than take some chances. I would absolutely want them to try some unique picks, but this would not be the game they would do so with.
Edit: Basically, I want Sega vs Capcom, Namco vs Capcom, etc and see them being more interesting over Nintendo vs Company.
In all seriousness, I can see why people might object to that idea, and even why it'd be impossible. But the Trainer mechanic is technically a part of Pokémon's roots left underrepresented by Smash, beyond the surface of the admittedly serviceable 
