The series wasn't planned out very well, and as I understand it, they had no structure in mind when they started doing it. I've actually never seen Seed or Seed Destiny 'cuz the mechas are so uninteresting to me, but the Kira Yamato character has a HUGE, HUGE fanbase in Japan, almost as big as Char, and bigger than Amuro. So I think that's why he was brought back even though the series was supposed to have a new protagonist/perspective.