Exactly, there are far too many variables that change even when you take him out of one slam (say, Wimbledon 2003), never mind completely eliminating him from history. Confidence and self belief are a tricky thing.
Without Federer, every draw would have been different, the mental state of each player/drive/motivation would have been different, tennis history would have taken a completely different course - in fact there's even a chance that without Federer around, Nadal would have never won a Slam since instead of designing his game to counter Federer he could have adopted a different style that might not have been so effective, or simply not had the same motivation to dethrone a dominant force early on. His mental makeup would have been completely different had the state of the game been totally different as well, there's no telling how he'd have done and the same applies to every other player of course, we need to keep in mind tennis is played by humans not machines who are unaffected by their surroundings.
Take Roddick for instance - without Federer around he'd never have felt the need to tweak his style and eventually change it completely, if Federer had never existed he'd have been a totally different player, both in terms of game and mentally.
In short, it's preposterous to believe that you can remove a 17-time Slam winner off the equation and assume everything else stays the same. Had Federer disappeared in December 2002, everything in the past decade of tennis would have been different, the game itself would have taken a different course.
Well I guess I get GSM's point better now. Of course it's impossible to apprehend all the changes involved, but I still find it a funny game to try