Just so I understand, I’m trying to compare two approaches:
#1-> Create a custom interface
copy app/design/frontend/default to app/design/frontent/my_interface (and also skin/frontend/default to skin/frontent/my_interface).
#2-> Create a custom theme
create a new directory app/design/frontent/default/my_theme
I think what you’re saying is that if I go with option #2, upgrades will be easier. Any future changes to magento’s default theme will be incorporated into my theme, and things should stay compatible.
If I create a whole new interface (option #1), I’m cutting myself off from any future changes to magento’s theme, even if those changes are needed to support new features. In other words, this is *bad*.