You know what is more important than beeing nr2 in RG?
Federer beeing seeded nr2 in Wimbledon, now that will be a hard nut to crack because Nadal got +3245 extra points from previous grasscourt results while Federer got only +720 extra points (+250 if he wins Halle). So that is 2500 points which is almost impossible to catch, but with Halle in the bag and Nadal going out in SF against Djokovic in RG and some other lucky results, who knows?
This is very important because Federer would have Wimbledon in the bag if he was to play Djokovic in the final, if Nadal and Djokovic play SF Nadal is out of the way for Federer to get that Wimbledon title. I think RG is more complicated even if he was to play Djokovic in the final and not Nadal.
Federer will most likely be seeded #2 in RG. Momentum and the numbers so far favor him. So does his confidence. Any small slip up from Nadal starting from Miami will be disastrous for him. Even if Nadal slips to #3, he could still be drawn to Fed's side. Nadal may want to avoid the Djoker but Fed has put himself in position to face both, especially nadal despite the matchup and head to head issues.
On clay, I will favor Djokovic over Nadal just because of the matchup and momentum. Nadal obviously over Fed on clay. I think Djoke and Fed are about even at best. On grass, I will favor Fed over both. Even last year, if Fed had won against Tsonga, I was almost certain he would have beat Djokovic which was what Nadal was hoping for. Alas, that's why the game is played.