2008 was the year where Federer had a record of 7-6 record against non-Rafa top 10 players (7-10 including Rafa) compared to 2007's 17-4 (including Rafa) and Fed started losing to players he mostly beat like Roddick, Fish, Blake, Karlovic, etc on HCs and on grass Fed didn't face a single top 20 player(s) before facing Rafa that year. Federer was definitely in his prime but there was a clear dip in form that year.
You say Rafa wasn't in his prime on grass back in '06/'07? So was Rafa in prime when, at 26, he lost to Rosol, at 27 he lost to Darcis and so on?
Goes both ways. Every great player benefits from previous greats' decline. Many had benefitted from Fed's own decline and Fed had to change racquet in late 2013 to keep up with the tour but you don't mention that.
Using the same argument, please tell me how many Wimbledons and USOs would Roddick end up with if not for Federer? How many HC slams would Hewitt and Safin end up with if not for the same player? How many slams would Murray end up with before his maiden USO victory in 2012? You're cherrypicking arguments here without mentioning the whole picture to suit your own agenda
If Federer faced 1 or 2 times slam champions during his domination period then so did Nadal during his domination on clay (1 time RG champion and that too "lucky" in Nadal's fan words). Soderling must be the GOAT for taking out prime Rafa then at his own backyard
Btw, I don't believe any player has played in a "weak era". Some of them are top heavy while some have more depth. Every player has its own no. 1, no. 2. and so on and there is NO objective way of comparing eras. All competition debates are highly subjective in nature.