Nadal is very good but to say he is better than Roger is just not so. They are very even but the contrasting style of play makes it interesting between them. People go on about Roger taking advantage of Rafa's injury, but Rafa took advantage last year when Roger had mono and back problems. Being able to win matches quickly and conserve energy is part of being a great player, and if Nadal's style of play curtails his career that's too bad.
In all honesty, I am a huge Federer fan. He is easily my favorite player atm. I honestly think all things being equal Nadal is probably better. Knee problems are much worse than a sickness like mono, Rog;s back problem was minor. When Nadal hits top form again he will probably beat Rog in three at the French and then again Wimbledon. Whatever happens here is up in the air, Rog is clearly the favorite but he has so many challengers, that are quality. Men's tennis is sight to see these days, so many quality players.