The Spanish tactician has been granted permission to talk to manager less Villa about the potential to become their replacement for the departed Gerard Houllier but Whelan is confident he will not lose his man to the rival club.
"My gut feeling is that he will stay with Wigan Athletic for another year or two," Whelan told Sky Sports News.
"I have had meetings with him. We get on superbly well.
"His decision is final. I can't make that decision for him.
"It's entirely in Roberto's hands. If he decides to go then it will be his decision.
"I honestly believe he will be one of the top managers in Europe in the next two or three years. One of the top six clubs will come in for him," Whelan added.
"He is a brilliant manager and an honest gentleman. I would be upset if we lost him. I rate him so highly.
"He has settled in so well. He has built a very young squad and I would be really upset if we lost him."