Hoping to see the X-Men, Spider-Man, mention of mutants or some other Marvel characters not associated with Disney in Marvel's Agents Of S.H.I.E.L.D.?
Well, that's not going to happen.
While TV rights and film rights do differ, showrunners Maurissa Tancharoen and Jed Whedon explain that their hands are tied regarding what they can use in the new S.H.I.E.L.D. series, so that means just characters and stories associated with what Marvel Studios owns will only be featured.
Tancharoen: We can't ever say "mutant."
Whedon: There's a database that's tailored to our show with the properties we can use as well as the properties that are owned by other studios and things that are flagged for major franchises. There are certain areas we can't go because we don't want to step on the toes of the movies. We've had free reign. There are certain rules in terms of the Marvel brand. Marvel is very focused on being grounded — and it is our world with the one twist that they're superheroes. There's no Metropolis, there's no Gotham. It's New York City and Chicago, and in the cinematic universe the process of powers is pretty young. They say it's only been a couple years since Iron Man in terms of our timeline in the universe. So the idea in our world that powers exist is new to the population and SHIELD's job description. It used to be keeping those things secret and that has now changed, so we're dealing with some of that.
Interestingly enough, there is a theory floating out there that Marvel may use the Inhumans to replace "mutants." Plans seem to be underway for an Inhumans movie, and Marvel Comics is launching a big Inhumans comic book event this Winter where people get exposed to the Terrigen Mists, which altered the DnA of the Inhumans, giving them powers of their own. So instead of being a mutant (i.e. X-Men), Marvel can get around that by making them Inhuman.