Unless Sony also is making a multi Marvel franchise fighting game: No.
There's currently multiple games available on the market that share the same characters (including Spider-Man and Guardians of the Galaxy characters, among others), and I sincerely doubt that Marvel would prohibit anybody from using Spider-Man and his associated characters even though there is a Spider-Man game on the way, or GotG characters despite Telltale working on a GotG game.
The thing that Bill Rosemann is referring to in particular is that there indeed do seem to be a few characters that Marvel does not have the game rights to. Namor the Sub-Mariner seems to be one of the prime ones there, and there's always been characters that Marvel didn't seem want to get used on and off (for instance, there was this Super Hero Squad online game made by Gazillion before Marvel Heroes, and they weren't allowed to use a set of specific characters, including Namor but also Bishop or Danny Ketch Ghost Rider; albeit Bishop appeared in Marvel Heroes and as a playable character in later Marvel games as well).