Connors-Borg was the main rivalry in tennis that lasted several years. Then, the main rivalry was Borg-McEnroe than lasted couple of years. After that, the main rivalry was McEnroe-Connors that lasted couple of years.
Federer-Nadal was the main rivalry in tennis that lasted several years. Then, the main rivalry was Nadal-Djokovic that lasted couple of years. After that, the main rivalry, as of now, is Djokovic-Federer.
PS Novak-Roger rivalry badly needs more finals at slams.
First of all, the Fed/Nadal rivalry rarely happened on hard court (and hard court is about 70% of the tour). There are only 2 years when Rafa and Fed played more than 4 times a season: 2006 (6) and 2007 (5). Only 3 of those 11 encounters were on hard (2 WTF and 1 Dubai). Fed/Djoko has lasted longer and has been predominantly on hard: 2009 (5 encounters), 2010 (5), 2011 (5), 2012 (5). So that has been a bigger rivalry than Fed/Nadal for the last 4 years. Interestingly 2012 was the first year that the Fed/Djoko rivalry happened OFF hard: 3 matches on clay/grass vs only 2 on hard. That's because the main rivalry in 2012 was Djoko/Murray (they played 7 times whereas they had never played more that 3 times a year before). Djoko/Murray is the rivalry of the future, not Fed, sorry.
Regardless, the #1 rivalry in the last 6 years has involved neither Fed nor Murray. It's been Djoko/Nadal (except in 2010). 2007: 7 encounters. 2008: 6. 2009: 7. 2011: 6. 2012: 4 because Nadal only played half the year.
In slams, careerwise, Fed/Djoko have played 11 times: 5 times at USO, 3 times at AO, twice at RG and once at Wimbledon.They've also played 11 times in masters: twice in Cincy, twice in Canada, twice in Rome, twice in M-C + once in IW, Miami, Shanghai. Only 2 masters where they never met: Madrid and Paris. They met twice at WTF. Fed led the head to head in 2006, 2007, 2008, 2010, Djoko in 2009, 2011, 2012.
Fed/Rafa have played in 10 slams: 5 RG (that's half the total!!), 3 Wimbledon and 2 AO, never in USO. They've played in 13 masters (8 times on clay): 3 M-C, 3 Madrid (on clay), 3 Miami , 2 Hamburg + 1 IW and 1 Rome. That leaves 4 masters on hard where they never met: Canada, Cincy, Shanghai (or Madrid indoor), Paris. They met 4 times at WTF. Nadal led the h to h in 2004, 2006, 2008 and 2011. Fed led in 2007. They were tie in 2005, 2009, 2010 and 2012.
Djoko/Nadal have played in slams 9 times: 4 times in RG, twice at Wimbledon, twice at USO and once at AO (note that unlike Nadal/Fed they've met in every slam). The biggest difference is in masters where they played each other 18 times: 4 times in Rome, 3 times in IW, twice in Miami, twice in Cincy, twice in Madrid (clay), twice in M-C + Canada, Hamburg, Paris once. The only master where they haven't met is Shanghai. They've met at WTF 3 times + once in Olympics. Nadal led the h to h in all years except for 2011.
