Annoying Video Game Helper: Stop knocking the demons off the altar, stupid CPU players! They only die permanently if you kill them on the altar!
Stop killing the exploding bugs, dammit! We need them to rig the teleporter!
Author's Saving Throw: After the botched launch of the rereleases, a patch was issued and the developers apologized. They also promised the first game's DLC characters (absent on the 8th generation consoles despite rereleases generally including all of the DLC) would be free.
Game Breaker: One that was acknowledged and fixed: Deadpool's teleport in the first game. Essentially, it works by going for a spot a certain distance from Deadpool in the direction he's facing: if there's an area the player is allowed to go at that point, then Deadpool will instantly move to it. If not, he'll go as far as he can along that path. Elevation doesn't matter. Nothing in the way matters. Because of this, if used smartly enough this can be used to - in addition to getting places the player usually can't - skip whole areas of the level as the player is fully allowed to go through walls, Insurmountable Waist High Walls, voids and rivers, even burning wreckage as long as there is something to walk on on the other side. In the sequel, Deadpool's teleport was unsurprisingly changed so that it does not go through things the player is not allowed to go through, and the range is decreased to boot.
Ronin's "Spine Teaser" power is absurdly over-powered when used on larger enemies. Just how over-powered is it? When fully leveled up, it can kill Dr. Doom with one hit.
The sequel gives this status to Storm near the end, where the nanites allow enemies to share powers with each other. Their powers tend to be either telekinesis, fire or ice, the latter two being powers Storm is immune to, making a good lot of the challenge in the later missions including the final boss fight with Nanite-Fury.
Doctor Strange happens to have a spell that has a chance of... instantly killing any non-boss enemy in the game by turning them into a box. A box that can contain GOODIES.
Thor is this in MUA 2. Of the 3 Purposely Overpowered characters: Hulk, Thor and Jean Grey, Thor is the most overpowered. Hulk is a tank but is purely physical and Jean is purely elemental and a Glass Cannon: both of them can run into enemies and bosses that resist their damage. Thor however, has as much physical damage and defense as Hulk AND can dish out as much elemental damage as Jean thanks to his lightning. He's pretty much a walking brick wall and no enemy in the game resists both his damage types. The only reason to not use him is a Self-Imposed Challenge not unlike the above-mentioned Storm from the old X-Men Legends games.
Hulk is even more overpowered in the first game due to the fact that unlike the sequel, he actually does have a health regen ability in addition to his powerful attacks. When put into his "Fury" boost (which increases his size and attack speed), he is virtually unstoppable.
Harsher in Hindsight: Deadpool's fight with the devs of the game has them threatening to make Deadpool DLC. This was soon before all of the DLC for the game would become impossible to unlock without console commands.
Black Panther and Storm being part of the "Double Date" bonus after their disastrous breakup in Avengers Vs X-Men.
Narm: Penance in MUA 2. Also a fair chunk of Mephisto's dialogue, with the use of "astral energy" instead of "soul" and Nightcrawler's Small Nein.
In the first Pro-Reg mission, as soon as you run into the White Star, one of them says in the whiniest voice imaginable: "It's a raid! Get to your positions!"
You know those big hulking... things you run into at the omega base? Seem kind of intimidating, don't they? Then you run into them again in Asgard, and they talk. And they sound exactly like you'd expect them to. Another enemy that suddenly talks in Asgard is the Clay Warrior. His "Halt! You Shall Not Pass!" might have been badass if you hadn't just spent a level one-shotting about two-hundred or so of his kind.
In the first game, one of Doctor Doom's victory phrases after defeating an enemy is "Finally! I have achieved my ultimate triumph!". When he says this after defeating Random Mook #284, it's either this or Mundane Made Awesome.
Porting Disaster: The new releases for PlayStation 4, Xbox One and Steam are being heavily criticized for being very buggy, crash-prone, laggy and unresponsive. None of these issues were present in their original releases. The updated graphics are botched and customers have accused Activision of cashing-in on Marvel's popularity while delivering a clearly inferior product. A patch addressed some of the worst problems, but others still remain.
They Wasted a Perfectly Good Plot: At the end of the First Game it's revealed that Galactus has sworn vengeance upon The Heroes and vows to destroy their planet for what they did to him during the course of the game. Sounds prime for a Sequel Hook right? Nope, instead all we get in 2 is a brief mention (that you might not even notice) from Thor about how he drove Galactus off when he came. also, Black Widow's betrayal was not touched upon in the sequel.
Tier-Induced Scrappy - Elektra and Blade in the first game were both considered pathetic - Elektra having no good attacks before level 22, and Blade having massive energy management problems. Not surprisingly, in the sequel, Blade was relegated to the last-gen versions, and Elektra was removed entirely.
The sequel has it's fair share of this, too: Daredevil doesn't gain any good powers, Venom has awful defense and low-damaging powers, and Penance had equally bad defense and a Game-Breaking Bug that prevented his unique mechanic, that his powers would deal more damage the more he gets hurt...granted, it was patched, but still.