I partially blame Spielberg's tendency to do 2 films per year (particularly in the 2000's) that seemed to prevent Williams from working with different people. And the accumulation of work with the prequels -and to some extent with the Potters.
We know he had some interesting offers that decade, like Disney's Treasure Planet... I seem to recall there were more.
Money could be a factor as well. He has said in many interviews that he's willing to lower his paycheck, but even at a lower cost he's still really expensive. I remember reading an interview with Simon Pegg and Nick Frost a couple of years ago where they said they wanted Williams to score Paul but that he was too expensive.
However, I wonder if he hadn't had all those Spielberg movies, the prequels and the Potters... Had he scored as much as he did? By 2005 he probably became exhausted and didn't want to do stuff that he wasn't that keen on, like Amenanbar's Agora, which would have been hella interesting. (though I think maybe he passed on it considering it was probably too similar too Munich musically, at least according to the final product)