Even though Nadal turned pro in 2001, it was not till 2005 that he 'arrived' winning his first Roland Garros in his first attempt. By then he had climbed to No. 5 in the world and faced some guy named Federer (who was incidentally the world No 1) in the semifinals. When Federer squared off, he had not lost a single set and had already dished a bagel enroute further bloating his persona against the first time French Opener.
Federer lost three sets to Nadal while winning just one. That was their third career meeting with both winning one match a piece. Nadal beat Federer @ 2004 Miami - in straight sets - for their first professional encounter. For rock people, that was on a hard court. Next year, same place, for their second professional match, Federer BARELY won in five sets.
So by the time Nadal's first Roland Garros came around (for their third meeting), Federer had a very clear idea where this was going LONG before anyone else did. Nadal was a near-nobody then. Add the two and the you have the spawning of an extremely strange kind of friendship with both having their own unique reason(s) to bond.
Federer's stature and his standing with the fans worldwide at the time kept the equation from skewing ridiculously. Even though Nadal beat Federer in the next five STRAIGHT encounters after that Roland Garros win (four on clay, one at Dubai), Federer STILL had ample juice to NOT allow it to 'spoil' the 'friendship'. As time passed, Federer's dominance on surfaces not called clay edged him past Nadal enough to allow Federer to dictate as a big brother leaving Nadal with no option but to 'yield'. Result? Closest togetherness that's possible between two people after the same carrot.
While on this journey both soon began experiencing bumps. Federer's dominance on other surfaces began to erode while his ability to reciprocate on clay diminished with every passing day. Nadal's tolerance for indignities or 'holding back' he had to endure because of the glaring glow of Federer's persona and draw worldwide (AO award ceremony) began to wane as his own fan base grew alongwith the number of 'significant' titles specially over Federer. The two factors created an uneasy calm destined to lose it's civil cover sooner than later.
It all finally came to head when Nadal demanded a more friendly schedule and Federer refused to offer even his most lamest support to the idea. Heck, just by keeping quiet he essentially shot it down - with disgust - and gloves were off.
Part of the reason for Nadal's request was to build some kind of face saving contraption in the wake of what seemed inevitable: His abrupt exit fueling a Federer resurgence.
For the two to find ANY friendly turf now, Nadal has to match Federer's Slam total. Without it, the 'loss' WILL haunt Nadal severely enough to block any durable patch up - even long after retirement.