Throughout the game, various characters are skeptical of Black Widow's intentions. Daredevil however defends her and is certain she isn't a traitor, mentioning that he fought beside her and were both romantically involved in the past. This serves as a reference to the Daredevil comic book series (later titled Daredevil and the Black Widow), where both characters co-starred together between issues #81 through #124 in the early 1970s.

Originally, the Mattie Franklin iteration of Spider-Woman was planned to appear as one of Spider-Woman's costumes, with even concept art being made of her. In the final game, she was replaced by Mayday Parker (Spider-Girl).

Ultron's more "dog-like" head design featured in the game, which deviates from artist John Buscema's original design from the comics, appears to be based off of a promotional image featuring a prototype of the Ultron action figure produced by Toybiz for the Marvel Legends "Legendary Riders" series of toys. The final version of the action figure would instead feature a more humanoid head.

Originally, Thanos was briefly considered as a boss fight, but he was scrapped due to being considered a low priority character at the time of release compared to someone like Galactus. Regardless, Thanos does make a cameo appearance in the good and bad endings, if the player saves or doesn't save Odin.

After Raven Software's previous Marvel game X-Men Legends II: Rise of Apocalypse, Marvel and Activision were both cautious as how to proceed with their relationship due to fearing X-Men as a franchise was "losing steam". Director Dan Vondrak, feeling as though most superheroes games are focused on the villains, instead pitched a game called "Marvel Supervillains". Inspired by Fable, the player could create their own supervillain, taking over a city and having a lair. Marvel really liked the idea, however Activision's marketing team was against the premise feeling villains were hard to sell, instead preferring the safer approach of playing as the heroes and leading to the development of Marvel: Ultimate Alliance.

Around February 2006, Marvel: Ultimate Alliance originally had the working title of "Marvel Legends". The name was likely changed to distance it from the X-Men Legends series and a toy line of the same name.

Much like the other versions of the game, online support was planned for the Wii version, but for unknown reasons, ended up being scrapped.

During the Helicarrier mission, the heroes have an encounter with Bullseye. Daredevil and Elektra specifically have unique interactions with him. Against Daredevil, Bullseye jokingly mentions: "Hope you aren't still angry over me killin' your gal Elektra." Against Elektra, Bullseye is surprised by Elektra still being alive, and says: "Just how many times do I need to kill you, sweetheart?" Bullseye is also curious as to how she came back to life, with Elektra commenting: "It's a long story, involving some really good friends... like Stick and Daredevil." These interactions reference Frank Miller's acclaimed early 1980s run writing for the comic book Daredevil, specifically issues #181-182, in which a conflict leads to Bullseye killing Elektra, along with issue #190 which features Elektra being revived.

In some pre-release materials for the game, including the E3 2006 trailer, Wolverine's default Modern skin during gameplay has him wearing a brown leather jacket. This jacket does not appear on his model during gameplay in the game's final release, but it does appear on him in the game's pre-rendered cutscenes.

With Nightcrawler and Dr. Doom being added as DLC, it caused continuity problems due to both characters playing major roles in the plot. To solve this, the game humorously lampshaded the confusion to explain why there are two Nightcrawlers and Dr. Dooms.

During the Murderworld level after rescuing Jean Grey from the Pitfall! arcade cabinet, Jean Grey's generic dialogue (when the player doesn't have Wolverine on their team) is used, but Nightcrawler has unique dialogue. Nightcrawler is at first confused why he is there when he is supposed to be missing, until it's implied by Nightcrawler that the Nightcrawler being used in Mephisto's Realm is a clone, and the one in the player's team is the original. Jean Grey then proceeds to speak of Nightcrawler as if he isn't in the room, leading him to assume she is experiencing hallucinations.

The boss fight with Dr. Doom instead has unique dialogue compared to other interactions with DLC characters. The game creates the plot twist that the NPC Dr. Doom time travelled from the future, and the Dr. Doom of the present begrudgingly joined the heroes to prevent the future Dr. Doom, who is powered by the Odinforce, from ripping apart the universe.

When playing as a character such as Colossus, the Thing, Luke Cage, or the Hulk, and pressing the X/Square/C buttons near Wolverine, the two characters will perform a Fastball Special. This is a recurring technique seen in other Marvel Comics properties where a large, strong character throws a smaller character like a baseball pitch to attack an enemy, being commonly done by Colossus and Wolverine.

Ghost Rider was almost cut from the game before release, likely due to licensing issues after Take-Two Interactive acquired the video game rights to the character earlier in 2006. Marvel only signed off on his usage under the condition he would not appear in any advertising material. Regardless, Ghost Rider still appeared on the game's box art and in trailers.

In the Omega Base level, a special piece of dialogue can be triggered between Venom and Mysterio, where Venom mentions wanting to protect the innocent from stray missiles. This indicates that the identity of Venom in this game is Eddie Brock, though alternate costumes of the antagonistic Mac Gargan and Angelo Fortunato versions of Venom are available.

Early on in development, it was considered that when a character wore an alternative costume, it would change their power set. Game director Dan Vondrak used the example of Iron Man as War Machine having a shoulder-mounted cannon. Ultimately, this idea was cut as it was deemed a "logistical nightmare" that could potentially overcomplicate all the characters' power sets.

Raven Software and Marvel had a good working relationship during development, which ensured that almost any character they wanted playable, as an NPC or cameo, made it into the game. In regards to how the roster was selected, Marvel pushed for the big name characters or characters they were planning to turn into major franchises in the future (i.e. Spider-Man, Wolverine, Iron Man), while also advocating for lesser-known heroes (Moon Knight and Luke Cage). Raven Software strongly advocated for Deadpool and the Hulk. To gather information on the heroes, Raven primarily used Wikipedia and comic books sent over by Marvel to research what characters to add to the game, and character picks were frequently shuffled around during development, even a few months before release.

Hulk was originally planned to be a playable character, and would have been unlocked during the Omega Base mission after a gamma explosion caused Bruce Banner to transform. According to director Dan Vondrak, there were a lot of back and forth talks between Marvel and Raven Software regarding his use, but due to licensing issues with Vivendi Universal (who acquired the video game license for the character to help promote the 2003 film "Hulk"), the playable Hulk and a Comic Mission for him were scrapped from the game three weeks before its release. Moon Knight replaced him in the PlayStation 3, Wii and Xbox 360 versions of the game. Despite this, Hulk appears as Bruce Banner during the Omega Base mission, likely a leftover from development, and during the "Doom's Day" cutscene. Hulk was later released as DLC for the Xbox 360 version of the game in May 2007, which Vondrak suspected was only then approved by Marvel to help promote the 2008 film "The Incredible Hulk".

In the Stark Tower hub world, if you interact with the NPC Wolverine and select the "You're pretty loyal to Fury" option, Wolverine talks about his relationship to Nick Fury, and explains an occasion where the Hand, a ninja clan who are apart of the Daredevil and Elektra franchises, brainwashed him:


This exchange is a reference to the "Enemy of the State" story arc from Wolverine Volume 3, issues #20-38.

The Punisher was originally planned to be included as a playable character, but was scrapped due to unspecified licensing issues.

Gambit and Psylocke were both considered to be included as playable characters, but they were ultimately scrapped to focus on a more diverse group of Marvel heroes besides the X-Men. Regardless, Gambit makes a cameo appearance during the cinematic "Doom's Day", and a corrupted version of Psylocke appears as a boss during the Castle Doom stage.

Originally, the Hank Pym iteration of Ant-Man was planned for the base roster of Marvel: Ultimate Alliance. According to the game's director Dan Vondrak, the development team ultimately decided against including Ant-Man due to issues with him being a character who constantly changes his size from big to small. They felt that with the camera already being zoomed out and overhead, it would have been hard to see him when he was shrunk down during gameplay. Despite this, Hank Pym appears in the final game as an interactable NPC.