How about, WordPress looks in the theme folder for a plugins folder and treats that exactly the same as the main plugins folder. If there are two plugins with the same name, the one in the main plugins folder overrides it.

That way everything you need is bundled, plugins within themes can be upgraded separately from the theme as a whole using the normal process, an alt version can be released, or simply created by the user, and maintained separately so theme updates don't break the update.

What else could you possibly want?