Wigan face United at Wembley today in the Community Shield.
Whelan told the Sunday Mirror: "David is a good manager, but it is going to be seriously tough for him to replace Sir Alex.
"Not only that, he is replacing the very best. That would be hard for anybody.
"What has happened with Rooney has made it even harder. David is his own man, but, if I was him, I would go to Sir Alex and ask him what to do with Rooney.
"There's nothing wrong in taking advice from Fergie. He has proved over the years that he is right most of the time, so there would be nothing wrong in consulting him.
"And Fergie knows Rooney a lot better than David will ever know him. United have a right to do whatever they want with the player because he still has a couple of years left on his contract.
"What they need to do now is either sell him or settle him back down.
"For me, though, it's gone too far this time."
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