I've noticed something about prestige of cities in a few games now - it seems very unbalanced.  If the soverign is royalty (or you higher a royal NPC, I think), prestige is suddenly much greater for your kingdom/empire to the point that you massively out-grow the other factions.  And there ends up being basically no check on this, because there are only a few improvements that affect prestige at all (and no resources, now that they were switched to diplomatic capital).  So either the royalty bonus needs to be reduced somehow, or there need to be more ways to boost a city's prestige.