If they were all the same age, and you want to keep the comparison strictly among these three players, you would need to look at it year by year using as reference what version of each player corresponds to each age (see below). One thing you can say is that Federer in his early peak years did not have to deal with someone the caliber of Djokovic 2011, Nadal 2010 or Nadal 2008. On the other hand, Nadal from the ages of 19 through 21 had to deal with Federer 2005, 2006, 2007, and Djokovic had to deal with all that plus Nadal. This is how I see it up to the present:
Great post, I had the idea to do the same with just Federer and Nadal. Here is what I see happening each year
Age 19 (Fed 2000, Nad 2005, Djok 2006)
Nadal wins RG, but nothing else, Federer and Djokovic don't win anything else either but Novak looks slightly better than Federer.
Age 20 (Fed 2001, Nad 2006, Djok 2007)
Nadal wins RG but maybe not Wimbledon yet (if we say that a prime Hewitt and Roddick are around) Djokovic possibly wins US Open, Federer wins nothing but emerges as a great talent.
Age 21 (Fed 2002, Nad 2007, Djok 2008 )
Nadal wins RG and Wimbledon, Djokovic wins AO, Federer doesn't win anything.
Age 22 (Fed 2003, Nad 2008, Djok 2009)
Nadal wins RG but loses Wimbledon and Federer wins it for his first major, he also maybe wins US Open (tougher competition makes him a better player)
Age 23 (Fed 2004, Nad 2009, Djok 2010)
Federer wins AO, Wimbeldon and US AND RG as well if Nadal has the knee trouble in this "reality", if not, it's Nadal's again
Age 24 (Fed 2005, Nad 2010, Djok 2011)
Toughest year to predict with Nadal having had a great 2010, Federer a great 2005 and Djokovic a great 2011. I'd say though Nadal wasn't playing great all of last year and didn't have to because of lack of competition. Federer wins Wimbledon, Nadal RG, Djokovic the AO, the US Open is wide open.
Age 25 (Fed 2006, Nad 2011, Djok 2012)
Federer wins RG beating Nadal (who played rubbish this year and Federer was very good in 2006) difficult to predict the rest but I'd say Federer would win Wimbledon as well.
So up til next year, roughly
Nadal 6-8
Djokovic 4-6
Federer 7-10