I was thinking recently about thinks like Planetstrike and the altered roster charts. My initial idea was that we could have "rulesets" for game systems, possibly as extra files that could be added later so that games masters could make their own campaign set, and to generally have them as a set of "requirements", but requirements that can add to the base number of units allowed (for example). That would let you pull it in when needed, let them be customisable, and let them work without requiring completely new army lists.
As for your second point, it's not one I'd thought about but it'd definitely be something that would be useful. I'd just call it "inherited races" where one army says "I inherit from and extend from this other main race". We'd have to take in to account file load order (to make sure that we didn't require the parent to be loaded first, which could end up messy), a potentially (although never literally) infinite number of inherits, and the possibility of cyclic inheritance (which is obviously a mistake) but the idea is good
And the final idea: Apocalypse "formations". We've not got a way of loading a fixed "formation" at the moment, but the "unit containership" that I have planned to handle things like Champions should also handle formations. What you'd end up with is a "Valkyrie assault group" that then contains a number of Valkyries and other bits. The Assault Group would then have requirements on it that would say (for example) "contains max 3 Valkyries" to validate the unit. If it is a fixed cost per unit then the container unit could contain the cost and the contained units could be free. If it was "50pts + cost of Valkyries" then the container unit would cost the 50pts, and so on.
I'm not quite sure how we'd handle the "utter mess of any army" part, though
Hopefully that makes sense