2005- Nadal won RG, 4 Masters and 11 titles
2006- Nadal won RG, 2 Masters and got to the Wimbledon final
2007- Nadal won RG, 3 Masters and got to the Wimbledon final
All those years are quite clearly better than Federer's 2003.
What's better? Getting to a final of a Slam or winning the Masters Cup? Probably the Masters Cup. But Federer's Slam results in 2003 were quite poor. So I guess all those three Nadal seasons do trump Federer's 2003.
Makes sense.
I think instead of Fed's 03, the OP should have included Fed's 10 in that place -- winning a slam, a masters event and a masters cup is clearly above Nadal's 05, 06 and 07.