I mean, Disney has outright said that Marvel is virtually autonomous. I know they could technically be lying, but it's something to consider. That and Ike Perlmutter being at the helm of a lot of the merchandising and licensing side of things is likely the bigger issue. The guy's notoriously hard to work with and has some, let's say controversial views, and has tried to sway the brand in certain directions. I have no doubt he's a major factor in the disconnect.
Basically a lot of it is ultimately Perlmutter's call, which is why I don't think MvC:I is a good predictor for how Sora in Smash would work out.
It's worth noting, yeah, there are probably many moving parts, but I can't imagine there aren't some general parameters which Disney has set and which Marvel is then freely able to autonomously operate under.
And honestly I forgot this was originally about Sora in Smash, lol. Well, yeah, he doesn't have ulterior motives to contend with, his inclusion, while complicated legally, would be straightforward in intent. Also it's an entirely different branch of Disney.
I feel it necessary to bring up Capcom as guilty in this situation as well. Looking at their past failure, SFV, it’s not entirely out of the realm of possibility to say that Capcom was responsible for the game being rushed. MvC:I has roster problems, absolutely, but the games problems go far beyond that. The game is fundamentally flawed in so many ways that lumping all up to characters is avoiding the rest of the problems that persist alongside it.
However, this does lead into a good Smash example. If this were a reboot, with less characters, it would receive Infinite levels of hate because to the vast majority of people characters are the most important part of the game. It may not be in from-the-ground-up fighting games where every character is original and is created to fit their specific purpose but in big crossover games like Smash and MvC they most definitely are.
I would place the blame on most of the technical aspects on Capcom, yes. They seemed to rush this and reuse as much as they could. Perhaps Marvel could've intervened should they have provided some of the budget, but I really could only guess as to the fiduciary details. Even should Marvel be overbearing about which characters they would allow on their side of the roster, there would still be a wide swath of characters in general that could've made the overall roster much less redundant and much more palatable, and I think the onus there is more on Capcom.
Like I said before, MvCI seems like it was a culmination of two companies' worst qualities.
But yeah, if and when Smash gets rebooted, they need to be super tactful, as many characters will be shed or changed in the process. They would definitely need some new compelling hook, or at least a lot of past fan favourites to offset the backlash. Though ultimately, if a solid, well-made game (which every Smash is), eventually people will accept it for what it is. And therein lies some of the difference from MvC:I, as even with a reboot, Smash would still be treated by Nintendo with the utmost care and respect (perhaps even more than normal). I think that would keep it from reaching MvC:I levels, but who knows, the Smash fanbase is pretty rabid and reverent of the roster.