Considering how ludicrously successful the cross medium-spanning superhero genre has become (mostly through the rise of Marvel and DC's filmic output), each and every one of the following developers must be kicking themselves that they didn't see it coming.
Partly due to the only truly brilliant superhero games being either Spider-Man 2 and its wonderfully fun swinging mechanics, or Rocksteady's phenomenal Batman: Arkham trilogy, there are only a handful of titles that really nail your favourite heroes' abilities.
In fact, superheroes created by and for the industry tend to be way better experiences overall, with guys like Infamous' Cole McGrath, Prototype's Alex Mercer or even God of War's Kratos all having awesome origin stories, dogged drives to succeed and morally grey compasses forever twitching to and fro.
Back to the lack of comic characters or movie properties making the crossover though, as the stigma of bad superhero games could easily have been averted if any of the following came to fruition. For all sorts of reasons they ended up on the cutting room floor, but that doesn't mean they can't be picked back up in the future.