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I'd like that too. I hacked it a little so that unlinked items show up with their own class, so I can control their appearance with the theme. That still doesn't allow linked items with linked sub-items but it wouldn't be hard to do.
There is at least 1 other menu replacement, but I haven't tried it (or recall it's name). Does anyone know if it does what mgcube wants (and what it's name is)?