Today, Homebrew does have some major shortcomings. The biggest one that comes to mind for me is the fact that it only seems to consider the dependencies of a package during its initial installation. That is, if A depends on B, installing A will trigger an install of B. However, after that, Homebrew will happily let you uninstall B (thus breaking A) without so much as a warning. Less critically, it doesn't track the fact that it only installed B for the purpose of making A work, so it can't help you clean up the left-behind-dependency cruft from the stuff you've since removed.
I don't disagree with your assertion about the state of Homebrew, but I wanted to point out the `leaves` subcommand.
brew leaves:
Show installed formulae that are not dependencies of another installed formula.
I'm not sure if it persists this state or simply calculates it on-the-fly by enumerating your installed formulae. But it does seem like the same data or functionality could be used to prevent your uninstalled-deps scenario.
Hmm... Interesting. I don't think that "brew leaves" truly solves the problem, though, since the list it generates will include explicitly-installed leaves in addition to no-longer-needed dependencies. It can help narrow the list of potential candidates for removal, though, which is nice.
