Griphphin said:
What is he doing to beat you? It sounds like he likes to rush you down, so remember that a well-timed push-block(advancing guard) can cause his last attack to whiff, allowing you to open him up and probably kill him as virgil and zero have really low health.
As far as good teams, go with characters that have easy-to-use combos and focus on opening him up. Wesker's magic series does a lot of damage and samurai edge low shot can otg. call in an assist to hold them in place as you do it (chun-li's y assist, lightning legs, is especially good for this) and you can combo it into his hyper for more damage.
Captain america is also relatively simple, his charging star plows through a lot of attacks and his magic series can be followed by a ground shield slash that otg's them and you can hyper off of it for very big damage (read: ~90% of Zero's health).
Aside from that, just keep practicing and learn to read his patterns and habits to exploit them for that one cr.L that can open them up.
Also, I don't know how he plays Zero, but if he doesn't keep his buster at level 3 charge to keep him normals safe, don't let him get away with attacking with abandon as a lot of his moves are more unsafe than they seem.
And Vergil's sword cross-up is unsafe on block, so make sure to punish him when you see that motion for the tell.
If he likes to keep going at you with constant attacks, then take advantage of characters that have zero frame hypers, like Dr. Strange's Spell of Vishanti or Hawkeye's Gimlet.
Lastly, online resources are your best friend for leveling up your game faster than your competition's.
Maximillion's "Assist Me" series is extremely informative...
...even if the comedy is a little hit and miss. Good stuff starts at 2 minutes 57 seconds.
Shoryuken.com is always nice for getting information on the game, be it the characters themselves [http://wiki.shoryuken.com/Ultimate_Marvel_vs_Capcom_3] or brushing up on the game's mechanics [http://wiki.shoryuken.com/Marvel_vs_Capcom_3/System_Guide]. It is a very valuable resource.
Lastly, GameFAQS has some good info because of the general skill level of the players there. Of course, it is GameFAQS so that means an elitist community more often than not, so I'd recommend just lurking/searching topics for relevant information. I haven't had much experience with Shoryuken.com's forums, but I've heard they are quite helpful as well for finding good tech for your character and general advice if you search through.