I don't know what standards I should be rating this Story Mode (by fighting game standards, it's perfect simply because it exists), so I'll just write my opinion:
I am disappointed by this game's story mode for several reasons:
1. This alternate reality bullshit was stupid. After all the pre-story comics, and the trailers indicating Regime vs. Insurgency, I expected them to go with the flow, and simply have the story take place in an original DC world where the players would choose who wins (Insurgency or Regime). But Superman was a straight up villain in this game, and they made it so we wouldn't feel remorseful in the slightest when we kicked his ass. They killed it with the time dimension stuff.
2. Just like in MK, when you beat an opponent, the subsequent cutscene shows that they have indeed been beaten. This is a gripe because, come on, Aquaman beating Shazam and the Flash? AQUAMAN??? Yeah right. And how are the originals beating their "dopplegangers" when, technically, the latter are more experienced versions of themselves. Makes no sense.
3. I felt all the villains were just thrown in there. Like, in the very first cutscene, you have the heroes fighting pretty much every villain in the game for no reason at all. How the hell did Doomsday come back, and how did they manage to beat him so easily? I expected more build up (and relevance) before they revealed a new villain in the story. Most of the villains were just tacked in fodder to beat up. lol.
But overall, the game had a story mode....period. And I'm conformed with that. By the standards of your average Justice League Animated Series episode, it was pretty good. Personally, I enjoyed the MK9 Story Mode more.