Thanos
No doubt about it, Thanos is the most dangerous being in the Marvel Universe. His base power level might not be that great, but he's the best tactician and wiliest mind around. Multiple times he's had ultimate power in the palm of his hands, and it's only through his own mistakes, not the power of his enemies, that he's been defeated. What normally drives Thanos is his love for Death, the Grim Reaper of the Marvel U. He will try anything to get her attention, including becoming God and killing half the Universe.
T. Bonne
Tron Bonne is one of the many Mega Man characters whose name is a musical pun - trombone if you don't get it. The brains of the air pirate family and controller of the Servebots, she builds many items that the Bonnes' use to bedevil Mega Man, but she's more of a nuisance than a threat. On top of stealing treasure, she has a not-so-secret crush on Mega Man, so perhaps her schemes are done partially to get his attention.
Venom
Blaming Spider-Man for all his problems, Eddie Brock wants revenge in the worst way and bonds with an alien symbiote that wants the same. Coming close to killing Spidey a few times, he routinely comes up short and has even been his teammate from time to time. While his powers are similar to Spider-Man's, he's much stronger and has a killer instinct the wall-crawler lacks. Though he's not some maniac, as Venom has a skewed sense of justice, and only wants to kill those he judges as guilty.
War Machine
One of Tony Stark's best friends, he came to take over the Iron Man armor when Tony fell into alcoholism. When Tony returned, Jim Rhodes still wanted to be a hero and was given his own suit of armor and the name War Machine. Though similar to the Iron Man suit, War Machine has a more militaristic style. It's armed with many extra weapons on top of the standard hand-stationed repulsor rays, and it includes the requisite strength and flight.
Wolverine (Adamantium Claws)
Perhaps the ultimate weapon, Wolverine is Marvel's #1 badass. Born a mutant and improved by the Weapon X program, he has a quick healing factor, an unbreakable skeleton with retractable claws, enhanced strength and sense of smell, and he's a one-man-army that plays by his own rules. Though an X-Man, he also frequents the Avengers and goes on his own adventures constantly. Though a bit of a grumpy Gus, Wolvie is normally a team player and has a heart of gold under the tough exterior.
Wolverine (Bone Claws)
There had long been a debate whether Wolverine naturally had claws or if they were part of his Weapon X improvements. Well Magneto answered that question by ripping the metal out of his body. Turns out he still has bone claws, that are entirely breakable, but can get the decapitating job done. Though eventually reunited with the metal, the adamantium-free Wolverine was part of the X-Men for a good while and that was his current incarnation at the time of Marvel vs Capcom 2.
Zangief
Emerging from the forests of Russia having beaten up his fill of bears, Zangief was a popular wrestler in his home country. At the request of his government he joined the tournament to bring glory to Russia. This mountain of a man has some complicated but devastating moves, including the pile driver. Though not the smartest, Zangief is a tough competitor and when mastered by a skilled player, is really hard to beat.
And if you're looking for more, check out Comic/fighting-game mashups that need to happen and The many faces of Wolverine.
