Just my opinion. I had mono about 5 or 6 years ago and I have never felt quite the same physically. It's quite a debilitating illness that can have a very long term effect on the body and never really leaves. It's not just me, many people have had this experience as well (see Robin Soderling).
Getting mono in the beginning of 2008 explains Federer's sudden drop in form IMO and why he has never been able to reach the heights he did from 2004-2007. He has never quite gotten over the illness, but being the great player he is the man is still a slam threat. Why else would he, at the mere age of 26, have such a noticeable drop in form compared to the previous years. I know I'll probably get some flaming for this but IMO this is the most likely explanation and its amazing that Roger is doing as well as he is these days.
Compare Federer to Djokovic, Murray, and Nadal who are all about the same age(26) that Federer was in 2008. They have games that are much more physically demanding and yet people scoff at the idea of them declining. It doesn't make sense to me that Roger would just drop off like that without an explanation.