I agree with the original post here. There are bonuses to every other city for the other two types level ups (mind you I still think upgrade towns should be called community, because there is a size of the city called town as well... but I digress).
Conclave - research bonuses and stuff for the entire empire.
Towns - food and health stuff for the entire empire.
Forts - garrison / troop upgrades stuff for the entire empire.
some of the bonuses for the empire that a fort can provide are better armament for troops. Or better yet quicker production times for troops say a cost reduciton of 50 hammers with the appropriate building (I'm just giving out a number, if someone has a better number please post it).
Perhaps better training that gives +5 dodge or +1 attack... I know that training troops at forts give higher levels and I think that should stay at the forts to reflect that but the other knowledge should seep to the other cities.