The 28-year-old was a helpless by-stander because of injury as the veteran Italian employed a central midfield trio in an attempt to shackle Germany at the Aviva Stadium last month, but saw his team collapse horribly to a 6-1 World Cup qualifier defeat.
Whelan said: "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."
He added: "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."
Trapattoni has spoken warmly of Wigan's James McCarthy and Sunderland's David Meyler, currently on loan at Hull, in recent weeks, and has finally answered the clamour to draft Norwich playmaker Wes Hoolahan into his squad for Wednesday night's friendly against Greece.
Whelan said: "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. It was okay 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."
If the speculation is to be believed, Trapattoni came perilously close to losing his job in the wake of the Germany debacle with the Football Association of Ireland issuing a vote of confidence 24 hours after a 4-1 victory in the Faroe Islands repaired a modicum of the damage, but by no means all of it.
However, the support from the dressing room was unequivocal in the immediate aftermath of the win in Torshavn, and Whelan insists it remains so. He said: "At the time, he had to take it [the criticism] because the results weren't right.
"We as players take the criticism on the chin. The FAI have now backed him, so hopefully they will just let him get on with it and hopefully qualify for the World Cup because that's why we are here and that's what we want."