That is an interesting point to bring up. Which is the cart and which is the horse?
Didn't the President start skipping the court for this surveillance before 2003? If so the conclusion of this article is completely false. I think a better conclusion would be that the judges on the court got upset because they weren't always being consulted. They started messing with some of the applications for warrants as a result.
Again, I would encourage people to read the article. The article contains one fact, the number of modified and denied applications. The conclusions reached by the article are completely based upon the conjecture of an unlisted source, who hates the NSA and compares Bush to Nixon.
I doubt that the Bush administration just started to change its techniques and approach some time in 2003. In 2003, three things happened: First, the US went to war with Iraq. Second, a Clinton judge got nominated to the FISA court. Third, Howard Dean got a lot of press and popularity for being an explicitly anti-war candidate.