An interesting theory on why Bush's wiretapping program couldn't go though the FISA court:

[T]he source of the intel tips is tainted. If you are generating leads from persons being held in secret prisons or if the info is obtained thru torture, then it makes it difficult to make a truthful declaration before a judge. Why not lie to the FISA court? That's called perjury. I suspect this explains the real motive for the refusal of the Bush Administration to go the FISA route.

This seems much more probable than the idea that Bush had the NSA spying on John Kerry, although since they won't tell us anything about this program we have no real way to know.