Athrun is better pilot whe he fights for something. Kira is honored because he can use SEED mode just for fun, while Athrun needs motivation. But when he do, he is as good as kira. He proved that on Junius 7 and now, he will have great motivation.

Archangel use Miriallia AND some guy as a CIC, so they can use Miriallia AND Meyrin.