But Jones said Cooper would thrive behind forwards who could share the spoils with the All Blacks.
"Will Genia is not there, so he is with a halfback he hasn't played with before, and Nic White is a little fella - my preference is for bigger halfbacks," said Jones.
"But at the same time, we saw where New Zealand's defence is weak in the last 10 minutes, against good feet, and Cooper is a feet player, a stepper. He moves and reads the game really well I think.
"I don't dispute Quade had problems under Robbie Deans, but I know the kid very well, he is very confident, he knows he will cop a bit of stick and he won't be a sook - he'll take it on the chin. He can really play, this kid.
"Where New Zealand will underestimate him is in this - every time they have seen him, he's been behind an Australian pack going backwards.
"This pack has stabilised - I'm not saying they pushed New Zealand around in Sydney, but they didn't lose anything and that gives Cooper a totally different platform.
"Cooper's never played behind a pack that was at least holding, or sometimes going forward. New Zealanders will see a different Cooper here."
Jones has immense faith in coach Michael Cheika who he said was the real deal, a tough enough coach but one who could also be a father figure to the players.
Jones said the All Blacks were still building combinations.
"They were poor against the Springboks, Argentina and us. That was some of the worst football they've played. They say they are here to put a team together and progress, to get a bit better, and that makes it ominous for us.
"The Northern Hemisphere will look at Sydney and say the balance of power is shifting, but I think it's too early to call that. The New Zealand players are outstanding and that's why there are danger signs for everyone else.
"And you very rarely find a wounded All Black unequal to the task and we may have made a rod for our own back."
The flamboyant Jones was a key figure in turning Australian rugby fortunes around, and snared the Bledisloe Cup with a win at Eden Park in 1986. He hopes his record as the last winning Wallaby coach at the ground becomes a thing of the past.
"It's the record I don't want to have and an indictment on Australian rugby," he said.
"There is no hoodoo about the place. It's a beautiful theatre but it's not the theatre that produces poor performances. It's the people who don't learn their lines."