Sad thing is, with the current climate and Marvel only using X-Men in comics not issuing game licesnes, a lot of classic MvsC Marvel characters would be out of it(mutants, Doctor Doom, etc) we will get the MCU characters instead.
I highly doubt this'll happen.
Assuming the game does indeed exist and is going to happen, I'm positive we're still gonna get those characters in the game.
While it's true Marvel/Disney has an aversion to pushing the X-Men too hard because of Fox, they acknowledge that they're a very popular set of characters they own, and WILL use them if approprirate.
For example, they have a MOBA style game called "Marvel Heroes" they've been doing for a while, and it has a very robust set of X-Men and FF Characters available.
Now, you may make the argument that this game was released midway through 2013, and the policy towards those characters may have changed since then right?
Well, the game got a massive update in 2016, so much so that they seem to be treating the game's new official title as "Marvel Heroes 2016".
Now, obviously they're not going to remove content. They're not going to scrub all the X-men characters out of the game considering people have been playing it for a few years now and would OBVIOUSLY miss those characters, but that doesn't mean they have to use those characters as marketing for the game. It makes sense to then market the game using the characters Marvel owns and only be like, "Yeah, the X-Men are in here" once you get into the game… but nope, if you check the website for this thing, which clearly says "Marvel Heroes 2016" at the top, it's still full of X-Men and FF characters.
The newest News piece on the site shows a costume for Colossus on sale, The "About" page for the game features 3 Character images and 2 of them are Fox characters, the "Game Guide" page features a series of videos called "Chronicles of Doom" featuring Dr. Doom heavily, and the list of Heroes page has a splash banner at the top that has Wolverine front and center along with (if you count Scarlet Witch) 6 other Fox characters.
Again, completely scrubbing the game of all of them would have been bad I think, but they also don't have to make Wolverine the main front and center hero on their heroes list.
So I think at bare minimum, the characters we have as the "Iconic" MvC roster members will be there.
Doctor Doom, Magneto, Storm, and Wolverine I think are locks. Deadpool is extremely popular and Marvel still uses him regularly in the comics, far moreso than the X-men or FF characters, so I think he'd be the next most safe.
The rest I could see being cut tho, which is unfortunate as I love me some X-23 and Phoenix… But I'll take it in order to have the rest.