... I think that the story arc angle and the game being designed for players to play established and pregenerated Marvel characters is where they guessed wrong. Most players I have ever played any RPG with groan at the thought of a pregen character. Gamers are a creative bunch and want to create their characters. There were character creation rules but they were really light on explanation and that might have been a stumbling block for other gamers.
While I can't speak for everyone, these are the reasons I wasn't a fan. To be fair, the story arc thing didn't bother me all that much. It's not that they weren't railroads (they were), but I rarely use published adventures anyway.
The character/character creation thing was a serious problem for me. I need real character creation rules, not make/pick a catch phrase and arbitrarily assign a die type. Additionally, the entire system regarding experience points and milestones. Not my cup of tea.
But I have to assume they, to a degree, saw this coming and hopefully will put something in their Hackers guide. Something with the same general system, but real character creation rules, hopefully.