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.
Broken Base: Long before Diablo III, the game introduced health and energy orbs to replaced the potions. This cause in uproar among fans of X-Men Legends who were used to the health and energy potions. When it was revealed that the orbs automatically home to party members when they walk near them and also gave a small amount of XP if you're already at full health, fans gave their full approval. Nonetheless, there are still some other fans who dislike the orbs.
Contested Sequel: People are divided on whether the second game is better or worse than the first: it's either considered better for the much better graphics, unique fusion super moves and branching storyline or considered worse because of the removal of several fan favourites like Doctor Strange, Ghost Rider and Blade, fewer alternate costumes (each character now has 2 instead of 4) and a downplayed focus on the beloved RPG elements the first game had.
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, reducing a good lot of the challenge in the later missions including the final boss fight with Nanite-Fury to nil.
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.
Of the 3 Purposely Overpowered characters in the second game (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, strength, and attack speed), he is virtually unstoppable.
In the second game, Human Torch's Flamethrower can cut through even bosses in seconds once he reaches a high enough level.
Doctor Doom is the charismatic leader of the Masters of Evil. Before the events of the game, Doom stole top secret information from S.H.I.E.L.D. on how to deal with Asgard should it ever become a threat. Doom then refined the plan as a way to steal the All-Father Odin's godly powers for himself. Through a series of clever diversionary tactics, Doom constantly stays one step ahead of the heroes as he gathers all the necessary tools he needs to defeat Odin. Colluding with the God of Mischief Loki, Doom successfully conquers Asgard and defeats Odin in battle. Not wanting to share Odin's power with his lieutenants, Doom implements a series of Uriah Gambits to have the heroes take out his lieutenants for him. He quickly consolidates his control over the entire world, using his newfound powers to crush any form of resistance, and brainwashing the remainder of Earth's heroes into his loyal servants. A brilliant mastermind who managed to ascend to godhood, Doom establishes himself as a truly diabolical genius.
Loki is a member of the aforementioned Doctor Doom's Masters of Evil, seizing an opportunity in the Masters to fulfil his dream of conquering Asgard. Despite being its newest member, Loki manages to quickly ingratiate himself into Doom's inner circle as his Number Two. Disguising himself as the traitorous Mandarin, Loki frames him for the chaos the Masters had caused in Atlantis. The deception worked, giving the Masters the necessary distraction to carry on with their plans undeterred. Loki then leads an invasion on Asgard with an army of super-soldiers and overthrows Odin as King of Asgard. Even as the heroes turn the tide, Loki has one final trump card — the Destroyer Armor. Supposedly defeated, Loki disguises himself as Nick Fury, tricking the heroes into freeing the armor from its prison for him. Upon revealing his deception he proceeds to hijack control over the Destroyer Armor and attempts to crush the heroes once and for all. A master of deception, Loki proves himself to be Doctor Doom's most invaluable ally.
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.
The re-releases for PlayStation 4, Xbox One and Steam were heavily criticized for being buggy, crash-prone, laggy and unresponsive. None of these issues were present in their original releases. The updated graphics were botched and customers 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.
The Steam release lacks a number of features which were added to the first Windows version which made the game more user-friendly. For example, it allowed access to all of a character's powers during gameplay by number keys, whereas in the new port you have to first assign powers to one of four slots, intended for playing the game with a gamepad.
Special Effects Failure: In the sequel, when one looks closely on Gambit's cards, every single one of them is rendered as a 10 of Diamonds; granted, this is only whenever you open up and look at him in any instance in-game. On the box cover however, he's holding his iconic Ace of Spades.
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, although depending on how much effort you put into solving the case, she was not a traitor at all.
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. (Although Elektra is returning for the third game.)
The Thing in the first game is also pretty weak due to having very slow attacks and powers that don't deal all that much damage. Thankfully, the sequel greatly improved his abilities, making him a much more useful character.
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) from functioning correctly, leaving him with below-average damage output across the board. Granted, it was patched, but still.