Board Thread:Questions and Answers/@comment-28898329-20160809202649/@comment-27701762-20160809203424

Because Flowey's philosophy of "kill or be killed" is still dominant. Asriel is still not quite Asriel properly speaking once he enters the battle. It takes the protagonist reaching out to him ("saving" him) to remind him and jumpstart his compassion again.

Up until that point, Asriel is still dominated by Flowey's sadistic idea of playing with others: let's mess with people to see how they react. It doesn't matter that he thinks the protagonist is Chara. Chara is just a new person to play with.

There is also the matter of taking complete control of the timeline. The protagonist apparently still has some minor control, and needs to be killed before Asriel can take over.