Oh, I've actually seen a few eps of this! (possibly more than you?) But it's been a while, so lets see.

The main character is Jared and he was possibly part of a government program to turn him into a super soldier or something? Jared can be sort of child-like in his interest in simple things but is really smart and manages to always beat Ms.... M? I think she had a full last name, but only an initial for her first name?

Presumably Ms. M is trying to capture Jared and bring him back to the secret program he escaped from but never really catches him.

Digimon?