Actually it was because, the director's wife hated Stellar, Cagalli, and Shinn in real life if I recall correctly.
Kira was ACTUALLY supposed to die. But, wife-chan hated Shinn so he told director to make Kira come back in Super Freedom which was later renamed Strike Freedom because, it would remind everyone of a certain group called Super Free.
tl;dr Explanation is irl drama.
In all clarity however, SEED would be one of best series if not for SEED Destiny. I think R2 brought down Code Geass by a lot too.
Hey who said R2 brought Code Geass down ? R2 is a lot more popular than R1 according to public popularity.