Two completely different players, each with their own attributes, obviously.
Yes, Federer has his backhand, and his natural ability to play his way out of trouble - eg an ace when needed. Nadal is just brute force. Neither is unbeatable however!! I would also say that unlike Nadal who's game makes him prone to various injury, Federer's game keeps him mainly injury free. And that counts especially with the new up and commers who come into any match vs either, with not a lot to lose and a LOT to gain.
I also have a feeling that Nadal has the ability to bore his opponents to death/sleep as he goes through his 'routine' up the other end. So different to Agassi who played FAST, not giving anybody time to regroup.