We need more fluid city development techs, and we need to be able to get at them from several trees, because in a normal game you are going to wind up developing a more stable military first

 

Sorry, not sure I see the point here, the whole point of being able to choose path means that this is a meaningless argument. You can develop a couple of levels of military and then switch to city techs.

Your argument is that you tested playing with one tree then came to the conclusion that the tree was limited and should be changed. I could do the same with Adventure tech and then complain that all my cities have no production or growth and that I am defenceless. I could then also argue that I could not even use the Adventure techs as my 1 man peasant stacks were too weak to complete the quests.

I would agree that generally Adventure and Military techs offer the most early - mid game, then city techs start to become more important mid - late game. A lot of city techs are not that exciting, given that a large part of of the game is "terraforming" and city building, it would be nice to maybe have some techs that allowed you to build more unique/larger buildings, things that make your cities standout. The biggest crime is really that the diplomacy tree is completely and uterrly useless outside of caravans. That requires more attention than the City tree.

With regards to materials, they are simply too plentiful. As well as population being a resource that has a maintenance cost so should materials. It would be interesting to see that the more buildings you have the more materials you need to maintain. Once you have built something, you generally have to pay something to maintain it.

Well, the issue with study-spam is the following: there is nothing else to do with the money. And we have too much money because of a bug, and the fact that the IA is too dumb to put the pressure on our resources.

The other issue is that the production buildings are too few: workshop, study, labs. The thing is, there is no incentive to use lots of materials for now, so building lots of workshops isn't viable. Similarly, spell research is already very fast at higher levels, so it's not like spamming labs is worth it. 

We need more options for spammable building. What about an expensive building that produces 1 metal for (say) 20 pops and 3 gold per turn? What about allowing players to produce all basic resources (except food) at a major cost? A horse breeder, an alchemist, traders, that would respectively produce horses, crystal, gold, but with moderate-to-high pop/upkeep prerequisites?

Pop and ultimately food should really be the core resources, and the majority of the rest should be obtainable in two fashions: via building construction (the main way to earn basic resources such as research, magic, materials, and maybe gold, less efficient for things such as metal, very inefficient for crystal), and from resources around the world. This would make for more interesting choices in city building, and, along with a fix to the battle rewards bugs, should prevent study spam from being a viable tactic.

Well, again, easy enough to mod...

Ok, This is where your entire point seems to lose all merit for me. You waited 88 turns to set up your second city? Personally, if I don't have an expansion city by at least turn 40, then the game has really taken a bad turn. One of the things that the beta does fairly well is allowing you to make specialized cities for tech research, arcane research, and material building. In the city described in the OP, there seems to be no defining specialization. A better strategy might have simply been to build two or three cities and specialized each, then you would have been able to have your capital with its lost library supported by like 20 studies instead of 7. 

That said, I think there is a point about a lack of city improvements, but I don't think it is easy to show with a level 3 city. As other posts have pointed out, you are focusing simply on the civics tech track and not unlocking any of the other buildings from the other tracks. If you look at what a level 5 city can produce, you will find that there are several choices for this level but they are mostly 1 per faction. This means that you really only need 3 or 4 specialized level 5 cities to house all of your high level improvements, as beyond this, you are only leveling for the city bonuses and the city pop, which can tend to have diminishing returns.

I understand your idea here, but since civ techs are not the only place to get compelling city upgrades, I am not sure about your conclusions considering that warfare and spell research also contain city improvements which are interesting. As for your second point, I wonder how many 4x games you have played if you believe that a city should always be producing city improvements. In general, the idea is not to simply build until there is nothing left, but to improve your cities in order to further your strategic goals. In some 4x games, it often feels like you simply build continuously because a single building takes so long to build that by the time you are finished you have access to another building which furthers your strategic goals for your city. In other 4x games, this strategy of continuous building will actually work against you as maintenance and other negative factors will cripple your faction.

From my perspective, your scenario is questionable since you are inherently limiting your experience by only building the one city and only research the one tech tree. I wonder under the same circumstances how long any other 4x game would run out of what you call "compelling city development options". In general, your conclusions ignore that after your 75 turns, you now move on to developing a new city while your old city starts to take on the new role of unit producer and citizen grower to deal with problems other than the simplistic goals of initial city setup.