I am currently playing MODOK, Shuma-Gorath and Sentinel a lot lately, and my main weaknesses are:
1- I am ass with Sentinel. 2- I got Shuma-Gorath in my team (although he can be pretty nice with Sentinel Force back up). 3- My team is main-centric. Once my MODOK dies, I've pretty much lost the fight. The whole team is centered around giving him backup.
Don't get me wrong, though, I've won countless fights after my MODOK died, it's just that that wouldn't happen a lot against pro opponents.