In marvel you can do everything perfect for a minute and have everything be undone in a matter of seconds.
Most of the characters who can mount a proper comeback in MVC3 are characters that you snap in early and kill on incoming. Phoenix, Vergil and Strider. Strider and Phoenix have really low health meaning the snap back generally pays for itself because the hit will generally lead to a kill. Vergil has no good incoming option and the quicker you snap him in the better (usually best to snap him in when the point character dies). If a Vergil is forced to burn XF1 and XF2 then you have done most of the work already and have essentially out played them.
If you are in a situation where a Phoenix is coming in with 5 bars + XF3 or Vergil is coming in with XF3 loaded then you didn't actually out play the other person... you made a critical decision error in not snapping in the anchor beforehand. You wanna know how Justin won EVO? He snapped in Phoenix and Vergil at appropriate times. Really the only character that came back on him was Magneto which really shouldn't have happened but it happens every now and then (not that often, he should've been able to contain him with Hailstorm and Wolverine pressure).
Basically the way someone out plays another person in MVC3 is this:
*Out play the other person in the neutral in the point character war fare. Get the hit, kill the point character.
*Mix up 2nd character. If you don't get hit then play neutral again until you get the hit again then snap in 3rd character which is normally the anchor. If your mix up was successful you do decent damage with a combo and end combo with a snap back before the 2nd character dies.
*3rd character comes in you apply your deadliest mix up to make sure they don't have time to breathe. If they get away then you need to play neutral but be aware of their raw tag to save their anchor or the DHC. Either way they are in a terrible position because they would either have to make a risky tag or they blow 2 meter. If you get the hit then you blow resources to kill the anchor.
*2nd character comes in again this time with less than half the health. Now you zone him out and space him... make him come to you and blow his X factor. It's about baiting the XF out, playing defense and then counter attacking. This is where most people lose because their defense is lacking. Once you have out played him here.. that's where you win the game (usually you are zoning out Doom in this case).
When something like this happens that's when you can say "yeah he out played that other guy". This strategy is how you dispatch of the standard top tier teams in the game (Morrigan/Doom/Vergil, Wolverine/Doom/Vergil, Zero/Dante/Vergil, Magneto/Doom/Phoenix, Viper/Dante/Strider, Nova/Strange/Spencer). The only time where you have to do something different is against a X/Vergil/Strider team where you basically just have to kill characters as they come and hope Strider doesn't come back on you.