Quote Originally Posted by Destai
I have a question that I'll probably come up with an answer to once I put it in writing but anyway; Why did Sephiroth wait till Aeris had finished praying to Holy to kill her? I get the feeling he could have killed her anytime he wanted to. Have I missed something here?
It was a tactical error that occurred as a result of hubris. He wanted to make Cloud suffer by forcing him to kill Aerith. He was pissed at Cloud for beating him in Nibelheim five years before, apparently, and it was too heavy a blow to his pride for him not to torture Cloud.

To his surprise, Cloud resisted smashing Aerith beneath the Buster Sword, and he had to step in to kill Aerith himself, only for it to be too late.