Mary-Jane Watson's character can only be unlocked by finding it in the overworld. Like many unlockable characters, you have to do a basic puzzle of some sorts to actually reach the token. In MJ's case, it's using super-senses to locate a chest, then using a rope-pull character to open it. And which character has both of those powers? Her long-time admirer and part-time husband, Spider-Man
In a simillar vein, the token for Black Cat, another of Spider-Man's more well known love interests, is also acessed by rope pull points and super senses.
Why is the Fantastic Four's Human Torch in the level "Red Head Detention" and teamed up with Captain America? The original golden age Human Torch, Jim Hammond, fought alongside Cap against the Red Skull, the boss of that particular level!
This is a case of Double Actor Allusion. Not only are Captain America and The Human Torch played by the same actor in their respective movies, but they’re also played by the same VA within the game.
Stan Lee has a cameo as a prisoner in the Raft. You'd think that the creator of various superheroes like Spider-Man being in a high-security supervillain prison was just Rule of Funny... until you remember that he also created a Rogues Gallery for all of those heroes. He's in jail for creating all those supervillains!
Now at first you would think the Red Skull being a part of all this is No Swastikas / Disneyfication in action. But remember, neither Doom or Magneto or anyone else ever interact with or even acknowledge Red Skull's involvement. Except for Loki, who probably doesn't care enough to look into Earth's history and thus doesn't know too much about Skull's past.
This is possibly the first version of Galactus's coming to Earth that actually explains why he came down in New York, of all places.
Confused by Deadpool's comment "Kingpin is offering low-price dental checkups! I HAVE NO TEETH!"? He knows he is a LEGO minifigure, and minifigures (technically, if you don't count printed expressions) don't have teeth.
Another way of looking at it is that since Deadpool constantly wears a mask covering his entire head, his minifigure doesn't have a mouth. Can't have teeth if you don't have a mouth.
It could also possibly be a reference to the fact that he's a Superhero (sort of) and Superheroes get kicked (or punched or stabbed) in the face quite often.
Though the characters in-game DO have teeth. You can see it in many of the cutscenes (like Tony Stark grinning) or even in the images of that very same mission (Captain America grimacing).
Some people have noted that certain characters, like Black Widow, have the Intelligence ability, while other smart characters like Spider-Man don't. However, the way it's used in the game is specifically as a hacking ability — which explains why spy characters have it while others like Spidey don't. (Still doesn't explain why Doc Ock has the ability and Superior Spider-Man doesn't, though).
Deadpool provides hints, cheats and color commentary. Of all the characters, he would know he's in a game.
Control panels can only be hacked by intelligent characters. Loki cannot hack these panels. Perhaps it's a hint that he's not as smart as he thinks he is.
Or that, as smart as he is, Asgardians don't use human computers very often. It'd be the same as showing a rocket engine blueprint to a neurosurgeon. Incredibly intelligent doesn't mean universally intelligent.
The fight with The Vulture has you tricking him into hurting himself by flying through promotional materials for Marvel heroes. When you remember Vulture's an old man, it feels more like you're taking advantage of his senility.
You can track down his character token in the overworld post game so that could count as sort of apprehending him... in a loose sense.
They tried to make the Punisher more kid-friendly by having his missions involve him going after polluters and traffic violators/reckless drivers... but considering that you're destroying people's vehicles, sometimes with them inside, it can seem like the Punisher has become a Knight Templar with an All Crimes Are Equal mindset who thinks traffic violators are on par with rapists and mass murderers and deserve to die. This supposedly more kid-friendly version of the Punisher seems to be even darker than other versions of him.
There is a massive HYDRA base under the Empire State Building. And it's full of massive missiles and magma streams. Now think about if the heroes hadn't found the base. How would those missiles have been launched, and what would their targets be?
Another awful thought: What happened to the crew of that captured S.H.I.E.L.D. sub? We never see them again after the fact.
