I think this anime learned lessons from previous games-to-anime adaption: KissSis and KimiKiss. This anime learned a lot from Kimikiss especially. Both works came from same game company. They are said to clone main character in the previous show. So, they choose to use game like setting, alternative universes.
I think the anime producers make the smart move to make the story sequence. They choose Haruka path as the first story. Since Haruka is said to be the most popular girl among Amagami gamers. The third episode broke the tv view record for late night anime.
Kaoru's story is in the second sequence, because it doesn't have any significance. She is said too "easy", so gamers are not too interested with her. However, she is stylish. She got "it". So, she's quite popular among non-gamers.
I think they want to leave the best to last. It may be debatable. The cover girl is the last in the story sequence because her personality is attractive in the different way.
