Most of the replacement voices sound nothing like the originals. Though this is no longer the case for XL. Most characters would be receiving their original VAs, but not everyone.
While really minor, Young Ben's Down-Special, which is Cannonbolt, uses the sequel look, even though this is pre-timeskip Ben.
They Wasted a Perfectly Good Plot: It's not uncommon for people to compare the story mode to that of a fanfic. We have the protagonists of many, manyCartoon Network shows, fighting all of the villains who teamed up, but the villains make some... Rather questionable area decisions (Vilgax in Marzipan City, for one), along with the reveal that the villain of the game is the remote control of the Narrator, which, while done in the manner of many of Cartoon Network's signature comedies, is entirely out of place in aCrisis Crossover, and one could argue that any of the villains in the game could have been better as the Big Bad.