Well, there is an article that viscant made about counter characters. Pixies>beam, beam>giants, giants>pixies. Their are also counter assist, which counter other assist. Psylocke loses to capcom, who loses to doom or tron (doom and tron are just about even), who loses to cyclops, who loses to psylocke and the cycle goes on.
If you play MSP, Santhrax would be the ideal counter team, because you have a Sentinel based team along with Capcom, who makes rushing down hard to do. And Capcom counter Psylocke.
MSP wins against MSS. You said it best.
Combofiend wins against MSP. Sentinel is too much for MSP. And IM’s beta assist counters Magneto, since it hits on both sides and Magneto always tries to cross you up.
MSP loses to Clockwork. Sentinel/Doom is already to much for Magneto. Storm is going to have hella trouble with Sentinel, especially on the ground. To make it even worse, Striders orbs are like anti rush-down and they win against all assist except Ken’s AAA. MSP is a rushdown team. Game over. Clock wins.
MSP loses to Team Guard (Storm/Sent/Cable). Team guard is very hard to counter. To make it even worse, the gimmick is the same, which is run away. MSP has difficulties with Storm/Sentinel. And you have a solid AAA in Cable to beat Magneto rush-down.
I have had sucess in beating Santhrax with Clockwork. Doom counters Capcom, and Sentinel is so free in the trap. All that leaves is Storm, which is left to Sentinel. Sentinel can definately beat Storm like 6-4. For these reasons, I believe Santhrax is countered by Clockwork.
I think that Row is definately the hardest to counter. But it hardly counters anybody. So if you hate gettign countered, pick Row.
Thats all I can think of.