Yeah, among other things it makes it really hard to project data across lists. Well, harder.
With one list you can do "give me GameObjects named 'Peacebloom' or Units named 'Bob'" (why you would want to do that is beyond me, but you COULD).
With multiple lists, you lose that ability (without additional magic that could easily break...)
Better to just keep one list and filter it as needed; it's not like performance is the bottleneck (come on, if you're doing it with FPS, that's at most what, 50-60 times per second? even poky old C# can keep with sorting a list of 100 or so objects 50-60 times per sec)