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.
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.
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.