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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Light blue Venom. It may have been a mistake or stylistic choice, given that his alternate color is in fact black, like the one in Marvel Super Heroes. However, has anyone seen a light blue Venom outside of Marvel vs. Capcom and Marvel vs. Capcom 2?
Orange and blue Spider-Man. (Likewise, his actual palette is available as an alternate color scheme, but only in original home ports.)
Ensemble Darkhorse: Captain Commando, Jin Saotome, and especially Strider Hiryu and Venom. The latter has the distinction of topping character fan polls for MvC3 DLC (alongside Gambit, himself a darkhorse), even long after the dev team stated that his fluid animations weren't compatible with the game's engine, whereas Hiryu (who skipped out on MvC3) had an inordinate amount of fan clamor which singlehandedly forced Capcom to work out a deal with Moto Kikaku in order to get him into Ultimate Marvel vs. Capcom 3.
Game Breaker: Duo Team attack (which allowed you to have both our characters on screen at the same time) when used with certain teams plus the Colossus assist.
Or for that matter the Colossus assist itself. Totally invulnerable, multiple hits, good damage, and gives ample opportunity to do any sort of combo you want it if hits. Psylocke, who has many of these same properties, is also quite popular. And once you learn the trick to get any assist you want, you'll have no reason to use anything else.
Any team involving Spider-Man, Strider Hiryu or Wolverine, at least in the right hands.
Gold War Machine/War Machine together on the same team is this, to the extent where if they do a Duo Team Attack and both perform a War Destroyer, the graphics start to glitch until the moves end.
Harsher in Hindsight: Considering Captain Commando only appeared in this game and the next one, Onslaught's comeback when he is confronted by Cap is darkly prophetic:
Your return will be short-lived, Captain.
Likewise for Jin's ending where he dies and Ryu expresses hope he'll be back, considering he only appeared in two more games after this (and the second game was a cameo in Ultimate Marvel vs. Capcom 3's Days of Future Past stage on a wanted poster).
Memetic Mutation: Some of Spider-Man's lines, such as, "One for J.J.!" and "Do your job!" (or alternatively, "DO YOUR GODDAMN JOB!") are minor memes in the community.
Narm: Chun-Li's ending in Marvel vs. Capcom: Clash of the Superheroes, where Charlie saves Chun-Li, but the way he kicks Bison off-screen looks more funny than dramatic. The other endings have varying degrees of Narm too, just watch.
Porting Disaster: The PS1 port omitted the tag team gameplay due to the system's limitations.
Tear Jerker: Hulk's ending, where Cap sacrifices himself to save the world, with the rest of the X-Men eulogizing him. Though this is sad enough, it's the frakking music that makes it worse.
Jin's ending, where he does the exact same thing is even worse when you realize he only appeared in one more game as a playable character.