Yeah it really forces you to look into those dotfiles you haven't read in two years, or that hack script you banged out in 5 minutes, and give them all a bit of thought. That "Just get it into my PATH so I can try it out!" impulse has definitely gotten the better of me a number of times.
I hear ya.
One of the things I started doing lately is not moving any dotfiles automatically when I get a new machine. After 3 days of moaning, I go and dig out just the stuff that I have noticed I am missing. (I do the same for firefox plugins and so on). It has definitely helped with the historical crud.