I face similar problems (slow to boot and shut-down etc....) with my Vista desktop. There were days when I wanted to toss it out the window. I do regularly defrag. I think my issues were (and still are) there are just too much crabs in the start-up folder. Much of which I did not intentionally put them there, nor do I know how they got in there. After I disable or uninstall some unfamiliar ones, boot up is a lot faster. Shut down is rather unpredictable. Sometimes quick, sometimes it takes forever.
I also disable all "auto this", "auto that".
That s aid, my Vista is not really "flying". I doubt it ever will! (I miss my XP)