Actually I like your implementation more. I hadn't thought about the levelling tree but something including a tall tower to make your capitol stand out from the other cities. Something perhaps upgradeable that is an outward symbol of the might of your kingdom/empire egs the tower of Ecthelion in Minas Tirith or even the Wizards Tower in MoM...
Maybe having a unique one to each race, that slowly grows as you level it up, maybe being tied in with the Tower of Dominion structure, which can be upgraded at each level of the city. Some suggestions for the different race's central buildings. It would also be cool if these structures provided some kind of defense to the city if it is attacked...
Amarians could have a giant wizard tower, that could add a wizard unit that can maybe cast some spells (increasing in level as city does).
Krax could get a big eastern style fortress with minarets, that would summon a sizeable force of Kraxis defender troops to guard the city.
Ironeers could have a large, growing fortress forge thing, maybe guarded by a few Iron Golems that would defend the city.
Magnar could get a giant Barad-dur style spiky hell fortress that summons demons of various varieties depending on its level.
Mancers could have a large trading palace, like an italian style Doge's villa, that brings in some well equipped mercenary knights to defend.
Men could get a regular ole castle/palace/thing, that would summon some elite pikemen guards to defend the city.
Tarth could get a more primitive, but very defensible looking fortress that would bring out some elite archers to defend the city.
Trogs could have a big building, preferably covered in chains that would unleash a Juggernaut or two on the enemy when the city is attacked.
Urxen could have a big, dark keep (obviously with sinister looking architecture), maybe that adds some extra elite defender units to the garrison.
Wraiths could get a sinister looking mage's tower, maybe with some ice and webs, that would summon an unreasonable amount of spiders.
Anyways, some suggestions...