His controversial comments stem not from worries about where to fit the high-profile trio into the starting XV but from his belief that they could be a disruptive influence on the squad as a whole.
Beale was sent home from the Rebels' tour of South Africa following an altercation with team-mate Cooper Vuna earlier this week, while Cooper was fined by the Australian Rugby Union last season after publicly criticising Deans and describing the Wallaby camp as a toxic environment.
"I think they've got a big decision to make with Quade Cooper, Kurtley Beale and James O'Connor," Jones told Live Sport radio in New Zealand.
"I don't know the best way to describe them. They're brilliant players at their best, (but) off the field they're probably not team leaders, and they are probably going to struggle with three of them being in the same squad.
"The three of them together in a team...if you've got enough of those blokes in a team they cause a few problems, and I think that's been the case in the past couple of years with Australia.
"That's where Robbie's got to make a decision on possibly which two he keeps and which one he makes expendable, because they all have had enormous problems off the field."
Both Beale and Cooper are in the running for the Wallaby fly-half berth for the opening international of the three-match series in Brisbane on June 22 but Jones is wary of a lack of consistency from the front runners for the play-making spot.
He has been far from impressed with what he's seen in general across the Australian Conference in this year's Super XV, either, although he still feels there is more than enough talent in the ranks to give the Lions a real run for their money.
"Whoever plays 10, and they've both (Cooper and Beale) got instinctive skills, the big thing they are both missing is consistency of performance and at Test level that's everything," added Jones.
"If you watch Quade over the last few weeks, (his improvement) has coincided with the comeback of Will Genia. Genia knows when to give him the ball and knows when the ball is good enough for him - he takes a lot of the rubbish ball himself.
"The Australian conference has been disappointing. I've never seen so many people stand still and catch a ball. There is a stark contrast in the level of play in the Australian conference compared to the New Zealand conference at the moment.
"But amongst that you've got very good players at the Waratahs, very good players in Queensland, who generally have been the bulk of the Australian side over the last couple of years.
"You've also got some young guys at the Brumbies coming through. Young (Jesse) Mogg at fullback could be a very, very good Test player. So we can put together a good team.
"It' going to be important that early on they decide on the style of play. That's probably been a worry with the Australian side over the last few years. They've tended to fluctuate wildly between different ways of playing the game. They need to come to a consensus on how they're going to play and I believe they can put together a very, very good team."