I've watched the Gundam SEED movies and re-read some of the manga to remind myself why I liked the series more than I did Gundam Wing or the UC series. I found that the characters were more likeable initially, seeming more like victims of circumstances beyond their control than terrorists and sociopaths (Wing). Unfortunately, as the story progressed, the writers focused so much on pacifist propaganda that they reduced the characters to mere mouthpieces for such propaganda, trying to impose their ideals upon their world (and the audience) in defiance of human nature and human survival instincts.
As I noted
here, the Three Ships Alliance should've been a group of Earth Alliance officers seeking to end the war by assassinating political/military leaders who wished to continue the war, like the German officers who plotted to assassinate Hitler. The Gundam SEED writers shouldn't have made them a third party seeking to end all wars, a plot point it shared with Gundam Wing which also made me lose interest in the series.
Another problem is that the writers tried to stretch the story across 50 episodes-- as noted, doing so resulted in the series having too many filler episodes and too many extraneous characters. Instead of sponsoring one series with 50 episodes, Sunrise and Bandai should've sponsored two series with 25 episodes each.