I am not going to get overly invested in this topic, but a healthy Nadal is definitely a better player than Federer these days, in fact a healthy Nadal has been better than Federer since 2008, with no exceptions really (the only times Federer has ever been better since the start of 2008 is the second half of 2009 and the second half of 2012, both when Nadal went down with injury for an extended period of time). Most players would rather have to go through Federer to win an event in recent years than Nadal, unless the event is the WTF. Nadal is also the player Murray has the worst record against of all the top players, Djokovic included.
Federer regained the number one ranking after Wimbledon. That is, he achieved the number 1 ranking due to his results from Wimbledon 2011 to Wimbledon 2012.
Nadal played all of his tournaments (atleast the major ones including masters and WTF that I remember) during that time period. Federer achieved the number one ranking BEFORE Nadal started his extended injury break. The fact is that Federer had been having a mini resurgent year where he had won many titles and had placed himself within reach of the number one ranking at Wimbledon. After the draw was released, if I remember correctly all Federer had to do was win Wimbledon and he going to be number one regardless of any other scenario (and that included Nadal reaching the finals). Injury had nothing to do it.
Now if you want to say that Federer only got the number 1 ranking due to his Wimbledon win which would not have occurred if not for Nadal's early loss, that his early loss was due to him being injured, let's recall a few things -
1) Nadal has always struggled in early rounds at Wimbledon. I'm not going to relist all the matches, you know perfectly well what I'm talking about. Until unless you want to suggest he was also injured in 2007 and 2011 during the first week.
2) Rosol was on fire, especially that 5th set. He got lucky and was just zoning. Happens even against the best of players (such as Rafa in this case).
3) As for Nadal being injured, I'm sure he was. However the thing is, I highly doubt his injury or more accurately, the pain that he experiences just magically cropped up within the 2 weeks from French Open to 2nd round at Wimbledon (with 2 matches at Halle in between). If he was in pain, he would almost certainly have also had it during the clay season and the French Open. And guess what? It didn't prevent him from ripping through the draw there and defeating Djokovic. Moreover if it was so bad that he would have thought that he has no chances of winning Wimbledon, he wouldn't have entered the tournament in the first place. The precise reason why he didn't enter AO according to him, he didn't feel he could win it. Yet Nadal judged himself fit enough to play Wimbledon. Unfortunately a combination of bad grass from + zoning Rosol sent him home early.
I'm not saying Nadal wasn't injured/in pain. I'm saying that attributing his loss ONLY to that is an exaggeration since he most likely won the RG with the same condition.
4) Murray actually played damn well in the tournament and could have possibly taken Rafa out.
5) Lastly, the roof came on in the final. Let's say Rafa makes it to the final in this dream scenario. The only time he has beaten Fed was in 2008 when he was at his best grass court form and had Fed mentally rattled and it STILL took 5 sets. Now add the infamous roof onto that, which as so many Fed detractors like to point out is the only reason he won against Murray/Djokovic. Well there you go then, the roof most certainly would have come on in the final and I don't think I need to remind you of their record indoors.
The point here is that winning Wimbledon for Nadal would have been a tall proposition regardless of whatever injury issues you want to attribute his loss to. He is NOT a lock at Wimbledon at all unlike RG.
Which brings me back to my overall point. No, Nadal's injury break had nothing to do with Federer getting back on top. He did that all by himself. Do not denigrate what he was able to achieve just because you hate the Federer fans around here. As hard as that may be for many Fed detractors to believe that a 31 year old Federer can somehow outperform a 25 year old Nadal over a 52 week period, it did indeed happen.
Don't get me wrong, I'm not saying that was "peak Nadal" either btw. His form was pretty terrible in many tournaments during that time period (WTF, Halle, Wimbledon, 2011 fall tournaments etc).
P.S. Apologies for the long post and I'm not trying to antagonize you either, just sharing my opinion on some of the often used arguments.