IMO there isnt a huge difference. 2010 is irrelevant as neither Djokovic or Nadal was a factor on clay that year, and in 2009 they were honestly equal factors (Djokovic played Nadal 3 times on clay in Masters semis/finals that year and pushed him each time, Fed beat a tired Nadal who Djokovic softened up for him once, then won RG where Nadal and Djokovic both went out early). I would say comparing Federer 2005-2008 to Djokovic 2011-2014 is the most relevant thing here. Neither played Nadal to win their RG titles, so even that part is nearly irrelevant.
The best ever Nadal on clay was 2008, 2010, 2012. So 1 Federer year, 1 lost year, and 1 Djokovic year. About a tie here.
The next best years of Nadal on clay were probably 2006, 2007, 2011, 2013. 2 Federer years and 2 Djokovic years. Again about tied.
2005, 2009, 2014 were the weakest of the Nadal prime/semi prime years on clay. So 1 Federer year, 1 Federer/Djokovic year, 1 Djokovic year. Again about tied.
So if that is your basis I see no real difference, and it changes nothing about my original stance. It is better to always go with results and achievements first regardless, as those are the most quantifiable ways to compare. Unless there is a very large and visible difference in playing level or competition, which clearly isnt the case here.
Lastly Federer's failure to win Rome/Monte Carlo was largely based on Federer himself, not entirely Nadal. He lost a very winnable final to Mantilla in 2003, went out early to Costa in MC or Rome (forget which) in 2004, lost to Gasquet after having a match point in 2005 which was prior to Nadal aserting any dominance on clay yet, lost to Stepanek in 2008, lost a final of Monte Carlo to his pigeon Wawrinka and went out another year 6-4, 6-1 to a nowhere near prime Wawrinka when Fed himself was at the top of the game. Wasted a match point vs Nadal in the 2006 final with a forehand UE, and yes while this was vs Nadal this has to be accounted to a failure by Federer himself. There are other examples, but Rome imparticular Federer is more at fault, than Nadal.