It's way dumbed down.
I'm not even a comics fan and I have a great dork affinity for this series. They remind me of the old TMNT and Simpsons arcade games I loved so much. This new one is the least frills yet. Every character only has 4 powers, which makes them all much more similar to each other. There's virtually no customizing anyone. There's even fewer costumes for them. Also, it's shorter than the old ones, and unlike the last game, which had lots of varied locations (Murderworld, Atlantis, the Skrull planet, etc.) this one is pretty much variations on city streets and dimly lit research bases.
The gameplay is unchanged, so I'm still playing it and enjoying that, but it's no question the worst in the series. Since I don't actually read the comics, the story pretty decent overall.