Primal, to prevent the building of multiple versions of the same vault giving more Arcanium, I suggest you link the Arcanium production to the Core Hub (level 2) for Vault I or level 3 (Vault II), 4 (Vault III) or 5 (Vault IV) levelup buildings. Although it means you will start accumulating the resource as soon as you get to the required level, the big advantage is that multiple vaults simply unlock more shop items - they do not make Arcanium points easy to get. And every city gets the Core Hub and level up buildings, and only one of them - humans could delete the level up buildings but what's the point? They give you bonuses and they are irreplaceable (unless deleting them allows you to rebuild them, it might do, doesn't matter though).
I've having an epic game of 1 Undead Conclave town with outposts against the world - my Sov and Bacco and 5 ghost units with Maces and 24 armor, so I did abuse the mechanic, but I would like it in future if you only get 1 (or 2, with Vault IV) of each local resource in the city each turn. 
How about a 1 turn Infection (Mage Savant), combined with Graveseal, Slow, Blindness, Curse and Wither - no armor low attack inaccurate enemies that always receive crits - joy!
