After Captain America: The Winter Soldier, Agents of S.H.I.E.L.D. pretty much stopped referencing the wider Marvel Cinematic Universe and became its own separate entity. It was also around this time shows like Daredevil and Luke Cage seemingly remained trapped in a post-The Avengers world and never really moved beyond that (not referencing the Sokovia Accords, for example).
In an interview with the AV Club, Agents of S.H.I.E.L.D. executive producers Jed Whedon and Jeffrey Bell were asked whether they were ever stopped from doing anything in the series, and the former started by recounting a fun plan for Enver Gjokaj following his return as Daniel Sousa.
"There was talk about Sousa having to do a detour undercover as a cop to fight in the streets in Avengers because Enver was in that film [as a police officer]," he explains, "but there was enough timeline problems. [Laughs.]"
That could have been a lot of fun for fans, but the conversation took a different turn when Whedon revealed Marvel Studios changed course on one character, in particular.
"We had a lot of ideas where we were—and I’ll say this, I don’t care—we were given the green light originally to use certain characters from Marvel, and started to break story based on those characters—[Coughs.] MODOK—and then they retracted it," Whedon said of Marvel Studios. "So there were a bunch of things that were going to get a little batshit crazy that were above our pay grade, in terms of the toys we were allowed to play with."
That could be taken as a sign that M.O.D.O.K. will indeed be part of Ant-Man 3, but also an indication that, as time went on, Marvel Studios started limiting who the show could borrow from the comics.
There will, of course, be some fans who get upset about this, but M.O.D.O.K. on a TV budget? You remember Deathlok, right? Still, it will be interesting to see if the producers reveal any more...