Duffy's document also supports calls for the All-Ireland Senior Football and Hurling Finals to be moved forward two weeks as part of a calendar overhaul.
The Monaghan man also believes that the inter-county minor grade should be changed from U18 to U17.
Duffy also says the club championship should be played in the calendar year.
Currently, the All-Ireland Club Championship series takes place in the Spring with the senior hurling and football finals staged at Croke Park on St Patrick's Day.
The director general's discussion paper points out that eight previous official reports since 2004 have attempted to address the twin issues of player burnout and the lack of regular club games because of fixture congestion.
"That we have failed to make adequate progress in the past is due to a combination of factors - notably a failure to implement decisions taken," says Duffy.
"If we care about the welfare of our players, as we claim we do....then we cannot simply talk about addressing these issues. The time has come to take decisive action."
Duffy believes that the abolition of the inter-county U21 Football championship, won this year by Tyrone, would help to ease the demands on third-level players during a period when the National Football League also takes place.
The director general says that the U21 football series should be discontinued after the 2017 competition.
The discussion paper also calls for extra-time to be played in all provincial and All-Ireland championship games and for the abolition of both the All-Ireland Junior Football and All-Ireland Intermediate Hurling championships.
Moving forward both the All-Ireland Senior Hurling and Football finals two weeks would see the former being played on the third Sunday in August and the later taking place on the first Sunday in September.
Other proposals include having an increase of the amount of two-code weekends during the National Leagues and the discontinuation of the Division 1 Football League semi-finals from 2017.
Duffy adds:"Are we going to practise what we preach by taking the welfare of our young elite players seriously and by providing the vast majority of our players with a fair and regular schedule of fixtures?
"The evidence that we are failing on both counts is irrefutable so let us not evade our responsibilities by pretending that these problems do not exist.
"We have reached a stage in our competitions' structures where something has to give.
"I believe that tradition and precedence are insufficient arguments for resisting change in the face of the challenge posed to our values posed by the issues of player welfare and the denial of fair competitive activity to the majority of our players.
"We should be fully aware that the GAA will continue to lose club players who are not offered a regular, planned and coherent set of competitive matches."
GAA director general Paraic Duffy has called for the abolition of the inter-county U21 Football Championship in a discussion paper on player burnout.