I posted this a little earlier, but wanted to see what everyone thought.
I think a possible solution to the 'too few resources' problem, is to add more resources, but vary the type. Just as apiaries/wheat/fertile land have different values (same w/ clay pit/marble quarry, and iron/ventri mines), maybe more lesser resourse nodes should be added. For instance, maybe a spent copper mine (from the 1st age) that only gives .3 or .5 metal per turn, but allows access to metal. Or City Ruins, which could add 1 material/1 tech per turn. In this way, even if secondary cities aren't getting prime resources, they are getting something, which would allow specialization and character.
Other 'lesser nodes' could involve mana (drained/dying shard node .5 mana, no elemental affinity), arcane lore (forgotten shrine 1 arcane/.2 mana), or food (natural well 1 food).
These could be spread separately, and in addition too the current nodes. I think that would add replayability and just make the game even more varied and, dare I say, fun.