Some initial thoughts on possible teams and fun names,  
Feel free to add your own.  (I will be trying out some of these.)  
 
CAP , Skrull , Hulk  = Captain Skrull Crunch  
Skrull , Dante , Wesker = Skrull Fuckers  
Tron  , Set ,  Zero = Dr. WAHWEE! 
Phoenix , Skrull, Dorm = BLAZE or Flame On  
Dorm , Ammy , Akuma = Angels and Demons 
Hulk , She-Hulk , SHUMA = GREEN! 
MODOK , Spidey , Iron Man = SCIENCE!  
Hulk , Storm , Dorm = Earth Wind & Fire.  
Thor , Doom, Magneto = MIRACLES!  
 Ammy , Felicia , Morrigan = Bitch Tits! 
Arthur , Deadpool , Haggar = King Shit Kicker   
 
 more to come.... 

Arthur, Joe, Ammy = Team "I'm too low to be hit by your high up attacks!"

Aw, I thought they were going to be the official names from the game or at least good made up names.  
 
Oh well, besides the too-obviously-pathetic-to-even-be-consider-half-serious names up there, Earth, Wind and Fire is the best of them