There are unique character dialogues in the game among characters based on who you chose for your team. Depending on the affiliation of the active character and the NPC to whom they're talking, their response will be different: friendly if both characters are X-Men or Brotherhood members, and hostile if it's an X-Man speaking to a Brotherhood member or vice versa.
In the New York City levels, some of the destroyed buses have a "Raven" sign on their sides and raven logos. This is a reference to Raven Software, the company who developed this game, along with its predecessor X-Men Legends (2004).
Beginning in this game, Iceman no longer wears a bandana on his head which makes him look like his Uncanny X-Men design and less like the Ultimate X-Men design seen in X-Men Legends (2004). However, Iceman continues to wear an armband on his left bicep, only this time it's a black armband instead of navy blue.
In the Weapon X facility, one of the rooms has a Newton's cradle on a table. This may be a reference to X-Men (2000) where Magneto had a Newton's cradle in his hideout, and he used his powers to get them moving.
The developers intended the game to have a greater sense of scale than its predecessor, X-Men Legends (2004), with a story where the X-Men would need to ally themselves with the villains known as the Brotherhood of Mutants to defeat a greater threat, the mutant supervillain Apocalypse and his minions.