I had the same feeling last year, so I started collecting all sorts of little interface fixes into a single script that I called the Stack Overflow Unofficial Patch, or SOUP for short.
Of course, SOUP is still very much a work in progress, and always will be. If you find something missing from it, I'm always happy to receive suggestions (and even happier to receive code; hint, hint!).
I do tend to take a somewhat conservative approach with SOUP, only including things that I'm fairly sure that over 99% of people would want (and which few, if any people would be likely to seriously object to), since they currently all come in one "take it or leave it" package. That said, I do think it could be a good idea to introduce more customizability and optional features into SOUP in the future, either through some kind of control panel, or directly by injecting custom (but non-obtrusive) interface elements into the SE design to control the features.