sorry for my absence in the last time. i'm quite busy with other things right now.
I'm actually leaning towards agreeing with Joseph II on some key issues here. I love the concept of upgrade chains, and felt it was a feature RoM never really used that well. I love some of the new building ideas, especially the earlier ones. But that's where my praise ends. I'm starting to wonder if AND 1.74 without the upgrade chains is actually more balanced than with it. I know 1.74 without it has a bit of a issue with over-production, but I think that could be fixed fairly easily. However, BuildingUpgradeChains still causes way too much gold to be earned... in fact, it puts a huge emphasis on buildings, and makes the tiles you work almost inconsequential. The static bonuses make any and every city a major gold city, and it's not hard to have even size 2 cities producing 16-18 net gold for your empire.
true, i've also noticed there is still too much gold. at the other hand research speed progresses a bit less exponential (which was the priority). the concept was first to reduce bare commerce yield excess (of which research beakers derive). thus many raw commerce boni were cut and/or changed to gold boni (i couldn't get rid of the bonus completely because some buildings would have no good effects at all... and RoM has a lot of buildings). i've tried to get the gold bonus controlled by city maintenance which is a direct counterpart for income. but: city maintenance scales with city number and distance to palace (i.e. empire size) while the gold income from buildings scales with technology level (defines what you can build). so there is no trivial way to balance these.
Perhaps the issue is that there are just too many buildings, especially once you hit the Renaissance and Modern eras. I get weary of seeing a list of 35 buildings I can build, each in less than 3 turns. I'd rather see 10-12 buildings, averaging 6-12 turns.
isn't this one of the core differences between RoM and vanilla BtS? RoM adds a lot of stuff - especially balancing problems.
I think a consolidation of the Bazaar and Market lines is in order. Also, Trade Ports shouldn't give both extra trade routes, and gold, since a trade route is generally ~ 3 commerce each already. Also, instead of having the science and gold buildings produce negative hammers and happiness, why don't they just cost citizens to employ and staff them? Perhaps each requires one or two citizens to staff, who can't then act as specialists or workers for your tiles.
the gold from bazaar and markets only compensates the previous commerce you could get from resources - which was huge if you could acquire some of them: example bazaar: the original RoM bazaar gave +15%

, +16

form 4 resources, +3

from 3 resources. i've reduced it to +10%

, +10

form 10 resources, no happiness bonus.
the market was reduced form +20%

down to +3

+ 5 form resources. also the +6 happiness from resources was reduced.
your idea about specialist to work these buildings isn't bad but also requires much higher city sizes due to have enough population to be able to work a small amount of them. big change in balancing -> much work, many problems at the start.
instead i thought of something else. the maintenance calculation of city cost is somewhat problematic i think. it seems it was originally invented to bound the power of large empires (maintenance scales with city count and distance to capital). what is realistically missing is a summand for city size (evidently New York will have to pay more for infrastructure then a small village. and the costs will be more significant then the civ IV maintenance factors i guess). so let's say cities of size between 1-10 pay 0.2

/size. above that they pay 0.5 per city size and beyond size 25 it's 1 per city size (as an example). commerce/gold buildings like markets can get a min population requirement so one has an mechanism to control gold income/expenses.
this is also the good effect that it lowers the over-powerness of mega cities.