At this point Seirin is struggling to keep pace with Seiho, they are still far behind, an Shutoku send their best player on the bench, it's really looking bad for Seirin.
Originally Seirin's defeat was supposed to be against Shutoku not Touou, but Fujimaki-sensei's editor convinced him to change it.
At this point, the story was clearly developing toward "Seirin, exhausted, can't keep up with Shutoku at nearly full power." I think the strong similarities and parallels between Seirin and Shutoku were the reason for this initial decision: Seirin was supposed to be beaten by the best version of them.
In terms of narrative development, having them lose to Touou and Aomine, GoM's ace, is more interesting thanks to the emotional component added by Aomine and Kuroko's shared history. But having them lose to Shutoku wasn't a bad idea; the rivalry and mirror constructions of the teams would have make it interesting as well.