I was reading the posts and it seems that an awful lot of the tweaks and rebalances on the strategic side of the game revolve around the dev trying to convince people no to spam cities - merchants take food so you don't spam cities for gold etc etc. This causes annoyance due to the fact that by and large most maps are random and you can't be garunteed enough of one resource to justify the 'conversion' buildings Frogboy has mentioned unless you make one for every combination (food -> mat, gold -> mat, mat -> iron etc.) which is just cumbersome. I recently had a game short on material if you can beleive it - crystal cramming my warehouses but material was literally more precious than gold.
That said, I have a different idea on how to dissuade people from spamming.
In GalCivII mining ship could venture out and secure asteroids and link them back home for a production bonus so I have taken inspiration from that and put together this system-
Create a new class of unit - settler - this one founds new cities and its cost increases each time you build one (differences increase as you go up)
Change the function of the pioneer - it founds an outpost - a sort of unimprovable city hub, can't build, can't train and doesn't produce an influence area, the only thing it does let you do is build improvement on any resource in the 8 surrounding tiles - that's it. It links itself to the nearest city by a trail (not a road) and any enemy unit standing on the trail cuts off that outpost. This is so that you don't claim resources on the other side of the planet - chances are someone will stand on the trail somewhere. Trails vanish with the outpost if it is destroyed. If an outpost come under an influence border it automatically is dismantled and it's resources return to a wild state - unless of course it's the owners influence, in which case the outpost will become redundant as the resources will switch to directly supply the city it's in range of, so it's up to the player to dismantle the outpost when it is useless
I think this will work as it will mean that your primary use for cities will be for territory (influence) and you can place them in strategically useful positions and use pioneers to link resources that will later join to the city when it has a big enough influence. This mean that if theres a gold deposit and a library to the south and a temple to the north but i really want to plug a mountain pass in the middle with a city for security, i don't have to place three cities - I can plug the hole and link up the resources until it is large enough to encompass the whole lot.
There we go - I now await the onrush of people telling me I am being daft.