I think there is solution for this. Some modders wants all these buildings to exist becuase they like C2C to be complicated and detailed. I understood this. But these are problematic in case of rules of CiV4 (by adding tons of gold).
Im talking building like hat shop, furniture workshop, magic shop etc.
Ok lets think about this: maybe these building should be bringing not
to your city but something different. Lets call it "Luxury". Which is responsbible for (example) happiness in your city.
And as for
production lets just leave some true commerce buildings like market, harbor, bank etc.
If we could make maintaining city happiness a bit more challenging to counterbalance it, hats, for example, could be made a luxury resource. With a more volumetric resource system this would be ideal.
But that wouldn't completely eliminate gold from the building either. The gold represents the taxation earned from the business. In many cases, the gold derived from a building is far too high at the moment.
I'm beginning to see the light on a purpose for some of Faustmouse's requested yield and commerce per pop tags. So long as they can be decimalized, which I've insisted on when considering the design, it would make sense for a building like a hat maker to produce something like .1 gold per population. There are higher sales in a larger city and while there may be multiple hat makers, the differentiation between such small scale businesses in competition has never been modeled in civ and would probably not be best not to be.
Without taking it to a resource and if we wanted to keep the effect localized, then hat makers, for example, could produce .1 happiness per population as well. Each pop brings with it a certain amount of unhappiness as it is, so this would help to compensate.
However, perhaps to help counterbalance that, as techs progress, unhappiness per population should increase because people who know something probably SHOULD be available but currently isn't get more upset than those who don't know what they'd be missing. This would mean that supply buildings like these will be necessary to counter this growing capacity for malcontent.
And finally about these upcoming Unit upgrade costs and maint. cost, it May reduce the number of units in the game. But the player will just kill off the older units for the measly gold they get and build the Newer Stronger units instead. The AI doesn't do this very well, if at all. If this upcoming Unit overhaul actually works and it can be proven the AI is swimming in gold afterwards, then by all means "tune down the gold". But hopefully we won't be hearing that old tired chant we get all the time, "the AI suxs in this Mod".
A step to take soon thereafter should thus be 'ongoing training' which enables units in cities to gain very gradual amounts of XP. I've rethought how to best go about this I believe, but regardless, once manifested into the game it should give quite a bit of motive to hold onto and upgrade units rather than having to build fresh green ones.
@DH: I most certainly don't try to limit growth in cities. It's one of the things I actually prioritize. This is because I prioritize production over nearly everything. Therefore, if a plot can't give production then I will almost always take it for as much food as it can provide so that I can get as many specialists as I can to provide the production those plots wouldn't.
Commerce seems to just fall into place so long as you can build your buildings as quickly as possible and set otherwise unused cities to building research or whatever is most needed there.
Thus again, production from plots become more valuable than commerce because at your option, production can BE commerce... depending on when in the game perhaps not at the optimal conversion rate, but effective nevertheless.
So if you undermine the plot values of cottages, they truly become useless, particularly since they are the best targets for raiders as said raiders can collect multiple gold drops from razing the plot many times before having to move on.
On Vanilla, any of straight CivIV, Warlords and BtS, the AI had a strong love of village improvements. This was one of their biggest and most vulnerable flaws in their AI.
) and you are out of the running for good. 
per city from the beginning on, it would also be boring. Managing gold is a huge factor in civ and if this gets completely taken out, it is like "cutting off the legs" of the game as you said.
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