Gundam Seed was mostly about fighting because of hatred and racism.
GSD however shows more of the manipulation during war from corrupt leaders and businessmen. This caused the 2nd war to seem to be forced in alot of the areas and disjointed.
Many people seemed to not like this way of doing the story. I for one liked this version better than the typical "I hate you so I'm going to kill you" way of fighting a war.
In my opinion most people who hate GSD are just spoiled Cagalli fans upset that Cagalli and Athrun broke up and Athrun got a new GF at the end of the series.