Marvel: Ultimate Alliance

According to the FAQ by oldschool312, the only X-Men team that provides an additional bonus is....
X-Men: +15% Max Energy
-Wolverine, Ice Man, Colossus, Storm.
Other than that, it's up to you, and your play style.

I recommend using Iceman, Magneto, Cyclops, and either Wolverine or Sabertooth (they're basically the same). Ice man's freeze beam is useful if your surrounded and need to slow or stop a few guys to make it easier. Magneto's Magnetic Toss power is basically like Capt. America's shield toss, which lets you cut through the enemies if you control it. Cyclops is great for area attacks using either Optic Explosion or Optic Beam, with the stick pulled back, which may also stun all the enemies it hits. Wolverine or Sabertooth as your last member is mostly for Might, as well as for heavy hitting, plus the fact that Storm is completely useless, Colossus doesn't do enough damage for his size and Nightcrawler is like a mix of Deadpool and Moon Knight, which isn't very good unless you have Moon Knight's Nunchuks and Deadpool's Healing Factor.

Use Magneto, Wolverine,Nightcrawler and Cyclops

Wolverine for his health/health regeneration and striking, Storm for her focus and energy(when she has lightning strike fully upgraded it is AWESOME! Whirlwind is helpful for big crowds), Colossus for his strength, and Sabretooth because he is almost the same as wolverine(Can't get better than 2 Wolverines)

I prefer a more well rounded team.

Magneto - Flying ability, Magnetic Explosion is one of the best radial attacks in the game, and Magnetic Beam and Shockwaves are great attacks as well. Plus Dark Energy is one of the best boosts in the game before maxing out your skills/costumes.

Wolverine - Excellent melee damage and his rage moves are great. Not much flexibility but he does well in most areas of the game, and his Claw Frenzy rage move is one of the best boss killers in the game.

Nightcrawler - His teleport skill can pass through a few obstacles in the game, and his Sword Whirlwind is a great boss killer/crowd killer. Plus he can slip out of trouble with Shadow Crawl if you get in over your head.

Colossus - Good melee and group boosts. His best assets are his strength ability, letting him use smaller enemies as weapons with grappling, and the inclusion of the Fastball Special with Wolverine (A fun move that X-Men comic lovers should appreciate)

This is all up to preference of course, but this is my favorite of the possible X-Teams.

I recommend using Nightcrawler,Cyclops,Iceman and wolverine.Because Nightcrawler can go invisible and it could help you out of trouble,Cyclops Because His Optic Explosion or Optic Beam can inflict damage to the bad guys,Iceman can freeze bad guys in there own paths where ever they go and Wolverine because of His strike and healing factor.

I recommend using Nightcrawler,Cyclops,Iceman and wolverine.Because Nightcrawler can go invisible and it could help you out of trouble,Cyclops Because His Optic Explosion or Optic Beam can inflict damage to the bad guys,Iceman can freeze bad guys in there own paths where ever they go and Wolverine because of His strike and healing factor.