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In the beginning of GSD, Shinn Asuka had been the main protagonist. We would see his story and missions. Athrun Zala was also like the 2nd protagonist. Soon, we see the outside stories with Kira Yamato and Lacus Clyne. Then during the series, we get to see more scenes with Kira and the Archangel.
To me, the change of main protagonist happened when Stellar was controlling Destroy in Berlin, Germany. Shinn and Kira were both trying to stop the machine, but it was Kira who actually destroyed it. When the news from PLANTs announce the battle, it just showed Shinn in the Impulse, and nothing about the Freedom and the Archangel. That sparked something between ZAFT and the Archangel group. Then there was the battle between Freedom and Impulse. This turning point made the Archangel look like the "good guys" and Minerva the "bad guys."
It is also clear of the change by the opening and ending theme songs. For example, the 4th opening theme song, Wings of Words, Kira is in the center of the three: Kira, Athrun, and Shinn. In the 4th ending theme, Kimi wa Boku ni Niteiru, it starts showing the characters from Minvera/ZAFT and ends with Kira and Athrun/Archangel group.
Examples:
 
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