Without going into too much detail, I think it's a combo of "Nadal is better than the competition Fed faced in his prime" and also Fed has legitimately deteriorated in terms of his confidence, his foot speed, his ability to come up with these 'special shots', his explosiveness, and perhaps his backhand. From whatever it was, if you really put time into studying his games 2004-2006 or so, then you compare that to the AO 2009, where he was playing a very high standard of tennis even, you cannot argue that his game has not changed in various ways. Combine that with Nadal and some of the other newer talents and you have what we're seeing now, to a large extent. Nadal *is* the greatest challenge Federer has seen right now, with Nadal where he is at this current point in time, but Federer also has his own problems to worry about that have more to do with his own game in isolation, and that would apply just as much even if he was playing someone other than Nadal. Call it mental, call it confidence, footspeed, whatever. I'll also state this doesn't denigrate Nadal's talent or playing ability or his great skill to state this, which I see as something fairly uncontestable if one would do the research and analysis. Nadal is an amazing talent and an amazing player and if he were playing now with Federer a few years ago, who could say what their h2h would be? I'm not saying in any way that even if Federer were in his prime he would beat Nadal now, and I'm not saying he wouldn't. That's a moot point. It's just not right to say that everything that's happening now is solely because of 'better talent in the field' and has nothing to do with semi-recent developments in Federer and various other factors I mentioned.
Further, none of us honestly know what's going on exactly in Federer's head, or what he thinks of himself and what's happening to his game and the results, or what he's doing to change in his off-time, and what he's thinking about, and what motivates him, and all the other personal facts that make up who he truly is, not some illusory image of him derived from brief fragmented press conferences and various other media interviews.
And for all we know, he COULD be seeing a sports psychologist all the time and has been for a while - pretty sure he too realizes there's something a bit off with his game (which might translate to something a bit off with his life in general, perhaps, something that maybe people who don't actually know him personally wouldn't recognize or realize), I don't think he needs the insightful geniuses at a tennis forum to tell him that - would such a proud guy as Federer publically announce he was seeing a PSYCHOLOGIST, if he were?