Can you explain us more about said dependency system? I've never been a big fan of meta-data files. I remember that chx wrote a very simple dependency system that adds about 30 lines of code and no meta-data files. It relied on a new _dependency() hook and that was pretty much it. Sounds a lot simpler to me but maybe I oversee some limitations? The limitation there is, you still have to load all the modules to find out what the dependencies are.
Except on install/configure time you don't need the metadata at all. True, you don't need the hooks as well. The separate metadata files, should help in creating distros, and tools for making decisions before downloading something. The format of the metadata is of no real concequence, as long as it is simple enough.