Long winded post full of spoilers coming up! XD
Actually, out of all the characters I think Athrun is the only one of good merits. What's Kira doing? Thinking that by just dearming the EA and ZAFT forces the war will end? Hostilites will still exist and another war will break out, every time Kira comes in, someone dies. It happened with Heine and it happened with Auel. Athrun while he may be confused, he knows what he is fighting for. He just doesn't know what path to take. Cagallis, his fathers, his own, but he knows what he wants.
Kira just wants to dearm the forces and let them solve the rest of their problems, he isn't thinking things all the way through. The war may have just restarted, but there have been problems since CE 23 when the world first learned of the Coordinator. So, what's been going on for almost seventy years isn't going to end just by dearming them.
And now, Kira goes out on attacking Athrun for personal feelings, not for any real reason. Yet, Athrun let Kira win, Athrun didn't go to SEED mode, he just floated there basically, and had a lot of chances to at least get away from FREEDOM. But that also brings up that Athrun can't go to SEED because he doesn't know who his real enemies are, and he doesn't know the full extent of what he wants his ideals to be. He is torn between love for his old friends, love for his new friends, and his love for PLANT.
Although theres never a white and black to what Kira and Athrun believe in what is the right thing to do. Athrun at least has the idea of wanting to protect, what's Kira doing? He just wants the war to come to and end without having to do any real work. It all comes down to "you have to work for your ideals, they're never handed to you on a silver platter".
Athrun wants to be there for Cagalli, but he also wants to be there for ZAFT. He's torn between what he grew up being prepared for and what Cagalli wants. His main problem is to many people want him, Kira wants him to be there for Cagalli and to fight alongside him, Talia and the ret of Minerva look up to him as a war hero, PLANT looks up to him as the man that saved them from a nuclear attack. It's just people being selfish and wanting to use him for their ideas and not letting Athrun decided what he needs to do, thus messing him up more.
Oh yeah, thought I might make this our GS/D discussion thread.