The 73-year-old manager has experimented with different formations since taking charge of the Men in Green in 2008.
Keith Andrews, Darron Gibson and Whelan were used throughout the majority of the qualifying campaigns for the 2010 World Cup and Euro 2012.
However, after a disappointing European championship this summer, the Italian has opted to use James McCarthy, while Norwich’s Wes Hoolahan and Sunderland’s David Meyler have been called up for Wednesday’s friendly against Greece.
“When the manager was first brought in, the board’s thinking was first and foremost to get us to a World Cup or to a Europeans, that’s what everyone wanted,” said Whelan.
“It was OK getting us there, it’s then what you do afterwards, it’s what you are going to do once you are there. That’s something we are going to work on and try to improve.
“He has fiddled about a little bit with systems and things like that, and that’s helped because since I have been involved and been playing, I don’t think I have played against another national team which has played 4-4-2.
“If it’s me or Keith Andrews or Darron Gibson or Keith Fahey who has been in there, we have been over-powered. We are playing three against two and we don’t get the credit that we deserve, really.
“We have taken a lot of stick, but what can we do? We are told by the manager to go out and play like this. It’s not for me then to go, ‘Hang on a minute, I’m not’.
“He’s the manager, he’s the boss and you do what he says because if you don’t, you are not going to get picked.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news