Well, he hasn't gotten everything he wanted during the past 7 years (remember Social Security reform, and immigration reform, and other major Bush initiatives that got nowhere).
So if he's been buying the cooperation of his own party for $50BN/year (approximate magnitude of earmarks in 2004), not sure he's gotten a good deal.
But now that Congress is under Democratic leadership, Bush's chances of getting much from Congress is even lower, and he doesn't even have any major domestic policy agenda left for his last year.
So after 7 years of ignoring the growing problem of earmarks, "now" he suddenly realizes they are a problem. Pure partisan politics.
That said, earmarks should be eliminated, so I guess better now than never.
Background on earmarks -
http://www.sunlightfoundation.com/earmarksFAQ