At the end of OotP Dumbledore says
“He chose the boy he thought most likely to be a danger to him,” said Dumbledore. “And notice this, Harry. He chose, not the pureblood (which, according to his creed, is the only kind of wizard worth being or knowing), but the half-blood, like himself. He saw himself in you before he had ever seen you.”
But this doesn't fit Voldemort's character, or more precisely it doesn't fit his situation. He has a prophecy about someone who can defeat him. Most likely it is a baby that will soon be born, and we know that he is aware of Harry and Neville, otherwise it would make no sense to speak of a choice.
It doesn't make sense for someone like Voldemort to choose one or the other instead of killing both. Even if he was 99% sure that it was one of the boys, he would still kill them both just to be safe.
If we want to call it a choice, it is based on opportunity and not preferences. The Potters were protected by a Fidelius. We can only hope that Dumbledore warned the Longbottoms and they also chose to protect themselves. Unfortunately for the Potters, the secret keeper was Pettigrew, which presented the opportunity to Voldemort to kill Harry (and his parents). Voldemort assumed that he would survive and would kill Neville at a later time, whenever he would have the opportunity.