Yeah, he isn't quite the same is he? It's the combination of getting older, accumulated strain on the body, and - perhaps - getting wiser. He understands that continuing to perform at those levels (2004-2006) would only drain him. I see him conserving his energies... and also conserving his abilities in order to increase longevity. In an interview, Federer has said that one of the reasons the field has been catching up the past few years, is due to their getting more looks at his gameplay - in 5 set matches and just general time on the court. They're seeing all that there is to him, and he's "no longer a mystery."
I wouldn't discount the mono issue, either. It's not like the flu; it's not some disease where you have it, and then you don't. It's contracted and stays in your system for a long time. I had it when I was younger: put me out of school for 2 months and there were days I couldn't hardly open my eyes. My performance in athletics has noticeably dipped since that incident. I'm not sure Federer's case was as severe, but it's still an important factor.