Hi Jeffro
Those shortcodes can be a nightmare when you change themes.

I changed theme frameworks recently for a small site and spent most of my time sorting out the shortcodes.
I think at the time I found a post by Justin T about locking yourself into a theme / theme framework by using shortcodes and I left a comment saying that I agreed 100%!

I use the Genesis framework on all my sites and they work hard at not duplicating WordPress core functions or tasks that are better suited to plugins.
Can be really frustrating when I have to play with non Genesis themes.