Surfaces.Both players are similar. They have the same weight, height and built. Grass and hard court are their best surfaces and clay is their worst. Both players serve are about placement and disguise. Both play 1-handed backhand and the forehand is their primary weapon. Both didn't need to exert much extra effort to win points. So what is it that separate them since Federer is more dominant and accomplished more ?
Totally different surfaces. in 90's, Federer's best surfaces would be clay and australian hard courts, IMHO.
Both Federer and Nadal would have been less successful on fast grass and US open hard courts of 90's than what they have accomplished last decade or so.