From what I've read, the first Seed was never intended to have a sequel, so when Destiny was announced, there was no real story planned, no outline, no structure...they just kept pulling stuff out of their ass, which would explain why it's apparently so terrible. I know I must see it someday, since it's Gundam, but I'm not looking forward to it.
Also, like in Seed, the mecha design are AWFUL.