I completely agree. It was super confusing figuring out how to access communities from other servers, and I consider myself a very tech-literate person. The Digg -> reddit transition didn't require understanding a whole new paradigm when signing up.
The part that was confusing to me is even if I choose “All” when searching for communities, it doesn’t find communities I know exist on other instances. This post helped clear it up for me (I have to search for it by link to add it), so thanks! I am worried this is going to trip up a lot of people though.