Berg named them as a defendant, so they had to respond. Basically, the FEC is claiming they have no authority or duty to investigate Obama's eligibility; and they do have a point. Berg was just coving all the bases because if he did not include the FEC, the Democrat party and Obama would have claimed that Berg did not include the FEC as a required party to the suit, which would have caused further delays.
Or he was afraid the FEC would step in, so he brought them in in hopes that they would claim they don't have jurisdiction. If the FEC is granted this motion, then they can't interfere with Berg in anything related to the case.