I think that the big difference between comic games and others is the sheer amount of pre-created characters over decades of stories. And there's a pre-set notion in the minds of comics fandom, including myself, that there's 'star' characters and 'everyone else. And everyone wants to play a star, even if it might not be the one you had your heart set on. There's a lot of baggage that can go along with that.
Relationships are already established and defined from the comics, with almost no deviations allowed for fear of a player making changes then dropping and future players not liking some of the changes a player made. I know that I've certainly passed on some of my preferred characters because I didn't like the in-game continuity for them.
And the 'star' characters remain relatively constant, but there is some shuffling of the 'A List' every so often, as new character get introduced in comics/media, and established characters get a popularity bump. Back when I first started MUing back in the late 90's/early 00's, it was easy to find a game where my personal favorite, Iron Man, was open and available. After the first movie,, though, his popularity shot through the roof and Tony tended to get taken quickly on new games. Same with 'specialty' games; there was a time when there were multiple games that were purely X-Men centric when the movie came out. Same with Heroes in that show's heyday.
I'm also not a big fan of the mixed universe games, despite how popular they are. There are serious power discrepancies between the top tier of DC characters and the top tier of Marvel. So, you end up giving Hulk or Thor a massive power boost, or you nerf Superman and Wonder Woman to scale them back.
I'd love to see OC games make a comeback for supers. Once, there were like 3 or 4 OC games running at once; now, we're pretty much down to Champions. But even then, I recognize that OC games aren't popular because of the amount of lore needed to be learned by a player to become functional in the game world, and that OC characters are stigmatized as being 'lesser' among supers players.
Another factor in supers games is what I call 'A Canon Of My Own'; the desire to create a new line of stories that suit the player's tastes where published canon falls short for them. I'm as guilty of this at times as anyone, I'll admit.
It all comes down to getting players invested in the game, and FC settings have numerous ways of getting that player investment right from the start.
So, how do you get player investment in an OC game? My main thought is to give them a way of making the character concept unique and special, even if it's an inevitable homage to an FC. Someone wants to play a Superman 'clone' character, that's fine; but give that player control of the lore surrounding the alien race they come from, have the player decide if there's other members of that race. Let players craft lore and legacies that can shape the game world and be passed along.
De-stigmatize OCs or homage characters; after all, the Fantastic Four are basically DC's Challengers of the Unknown with superpowers. Both Superman and Captain America share story and power beats from the 1930 novel Gladiator by Phillip Wylie (scientist creates a formula that turns his unborn son into a superhuman with tremendous strength and the ability to leap tall buildings). Batman's tone and concept are taken from Zorro.
It's certainly possible to create a general focus supers game these days; X-Men: Divergence certainly shows this. I think the keys are 1) Manage expectations, 2) Encourage player-centric lore, and 3) Patience. This would be a game that's going to require a lot of staff hand-holding and encouragement, will probably never be as big as one of 'the big boys', and will take a long time to grow into stability. Like a couple of years, rather than months. And I can understand a lot of devs not wanting to commit that amount of time to a game just just get a solid return in the player base.