Shani Andras, Orga Sabnak and Clotho Buer in that order. The Earth Alliance Federation's Biological CPU pilots. These three posed as a great annoyance to both Kira and Athrun even while in their Seed mode.
My favorite character is Shinn Asuka because he strives to be the best of his ability and is loyal to his beliefs. I like how they made his personality break out with anger, but still have a soft side after the tragic event that happened in Orb. His skills grow with the constant anger in his heart, while he still remains kind by carrying Mayu's cell phone to remember the past.
Kira and Athrun... Why? Cuz they make the best (yaoi) couple... They're against each other (at the start of SEED), but still thinking of the other... They make true best friends... And somehow, I can relate to them...
Kira, Athrun, Mwu, Murrue, Lacus, Dearka, Meyrin, Mir. I love them all, but if I have to pick one, it'd be Kira because he is a pacifist, and he has a good heart. The hardships he goes through honestly makes my heart break, and I know I'm biased here, but I like how he's kind of OP ;)