That's easy to explain.
This batch of Gundam Meisters are not selected for piloting ability. There are far better pilots out there. These pilots were selected because they believe in what they are doing, and continue to do what they needed to do without being told. They will work for free, they will work even if CB was destroyed and they were the last ones alive.
Setsuna is not as experienced as the other three Meisters corabat wise, but no one onboard the ship is as dedicated as Setsuna. The best part? Setsuna is not a follower. He isn't doing this because someone told him to. Setsuna's past made him painfully aware that in the end, he is the only person who can decide what he wants to do.
Setsuna wants to be GUNDAM. As it was spoken, so it shall be.