I just watched the 1999 Wimbledon final between Pete and Agassi. Agassi was playing about as well as I have ever seen him play. The amazing thing is that not once did I think Agassi had a chance to win the match. What happened? Pete at the top of his game wins in 3 sets.
I feel the same way watching Agassi play against Federer, but less so. Agassi still manages to bother Federer here and there on Federer's service games.
Now to compare Pete and Federer, I believe that a fast hard court and on grass Pete wins 8 out of 10 times. Truth is it doesn't matter who Pete is playing on those surfaces. His game is all about winners; he plays against himself. On a clay-court I'd say Federer wins 8 or 9 out of 10 times. On a slow hard-court I give the edge to Federer winning 6 out of 10 times.
It's all about the surfaces!