Yea he was injured so that may have played in a role on one of those years but he still should have cancelled Thailand and played Shanghai instead. It is just no comparison between playing a 250 and a Masters and I don't understand the choice to play that tournament instead of the one that awards much more ranking points. I'm not talking about Doha or Halle. I'm talking about Thailand, Rotterdam and Gstaad. Those three could have been placed on the chopping block in place of more important tournaments.
It's not fair to say he didn't have Federer's strike rate in majors since no one has really, and the participation in the Masters is not hindering them from winning majors. Federer still played the same amount or more tennis than Djokovic, but he was doing it in mostly minor tournaments. He has much more 250 and 500 titles than Djokovic, but Djokovic has more Masters. That's the trade off.
To me it seems you both guys forgot how the tour changed since 2004-6. At that time there was no obligatory Masters 1000 and differences between the categories were much more shallow then today. You are comparing Masters and 250 from today view, not from then point of view.
To put it into perspective, there are every players who reached #1 since 2000 to 2006 (and in case Federer is #1 I also use ye #2):
Sampras 2000 - 2 ATP 250 (played just 12 tournaments whole year)
Safin 2000 - 8 ATP 250, 7 ATP 500
Kuerten 2000 - 5 ATP 250, 3 ATP 500
Safin 2001 - 9 ATP 250, 3 ATP 500
Kuerten 2001 - 5 ATP 250, 3 ATP 500
Hewitt 2001 - 6 ATP 250, 2 ATP 500
Hewitt 2002 - 3 ATP 250, 3 ATP 500
Hewitt 2003 - 3 ATP 250 (played just 10 tournaments)
Agassi 2003 - 5 ATP 250
Ferrero 2003 - 4 ATP 250, 3 ATP 500
Roddick 2003 - 8 ATP 250, 1 ATP 500
Federer 2004 - 3 ATP 250, 2 ATP 500
Roddick 2004 - 7 ATP 250, 1 ATP 500
Federer 2005 - 3 ATP 250, 2 ATP 500
Nadal 2005 - 8 ATP 250, 3 ATP 500
Federer 2006 - 3 ATP 250, 2 ATP 500
Nadal 2006 - 5 ATP 250, 2 ATP 500
All of them played a lot of non-Masters/GS/WTF tournaments. Actually if we count only full seasons Federer is the one who played least of such tournaments. At that time it was normal and expected to play 6-10 such a tournaments a year.