Berrick Barnes has been handed the No.10 jersey while Cooper has also been overlooked for a place on the bench.
And Elton Flatley, who won 38 caps for the Wallabies and featured in every Test against the Lions in 2001, reckons Cooper needs to mature as a Test fly-half.
"Sometimes in Test matches you have to be a little bit conservative," said Flatley.
"Super Rugby is a little bit looser than Test match footy and just by getting out and playing more Tests he'll start to learn that."
But Flatley reckons Cooper is a unique talent and should be utilised somewhere in Robbie Deans' backline.
"Obviously Quade didn't have a great World Cup and he'd even admit that, but he's still a pretty young guy.
"He's still got some development in his game in learning to control games and even sometimes underplaying his hand.
"When he came back for the Reds he played really well by doing all the things he's really good at but even by underplaying it a little bit. Long term I think we'll see him as the Australian No.10.
"He's got that X-factor and he needs to be in the Wallaby team."