That's an interesting subject you have here, im gonna put some thought into real and useful ideas for this.
However right now i would like to say that there are some of the vanilla improvements that are simply not useful for me and i never pick them.
For conclaves 3 i always pick the oracle, they have lots of research buildings to be built and the only time that i put them to generate research is when i have basically built everything there is to build and that means the city has an incredible amount of research to need any more.
for conclaves 4 i almost always choose amethyst vault, as crystal is most of the time scarce, when i do have the good luck of having 2 or more crystal resources in my power i build the academy, i never build the university, i always try to have my unrest at very low levels for it to be an issue.
for conclaves 5 i feel most of the bonuses for conclave 5 are bland, i almost always choose either the bathhouse or the pyre, tower of magi is useless as a fortress beats a conclave in everything for unit training.
Suggestions for conclave: You could maybe add a path of improvements that are something like the tower of the magi, meaning making the conclave a viable unit training city.
For towns 3 i almost always build the grocer, however sometimes i do build the slums if my town has abundant food supplies, this is to get the mint of ruvenna as soon as possible so money ceases to be an issue, i almost never build the warehouse as i don't really think money is an issue most of the time and the gildar production of tows with their buildings is good enough for my needs.
For towns 4 i almost always build the almshouse for my first town(since fame is kinda hard to get) but i feel none of the buildings are really useful, i build the embassy in captured towns or any other town i might settle latter in the game or the Governor's Office, but as i said i feel this tier is kinda weak in benefits.
For towns 5 i always build the mint of ruvenna, the +2 production for a tier 5 building is weak and the mint most of the time will provide more gildar than a Lendinghouse.
Suggestions for town: i would suggest adding some nice bonuses to tier 5 so they become a real alternative to the mint of ruvenna, i would suggest something to help the town grow in tier 4(like food bonus in town).
for fortress level 3 i almost always pick strike garrison, in some cases i pick infirmary but i never pick the watchtower as i feel the bonus it provides is very weak when compared to the other 2.
for fortress 4 i almost always choose the prison, my capital is always a fortress, this means all the unique unrest and growth buildings go here and that also means Gallows is useless to me, i understand gallows might be useful in secondary fortresses, as for the mining guild i sometimes pick it if im lacking iron resource in my territories.
for fortress 5 i almost always pick the throne, 30% global unrest is a very very powerful bonus and in comparison the bonus the arena provides is very weak( i mean the sacrifitial altar gives 1 attack and 2 hp or something like that) and by the time you have a fortress tier 5 you probably have all the bonus to trained units buildings, meaning it feels even weaker, also the Underforge is also very weak, a tier 5 fortress is going to have its production through the roof and an armorer built on it so it makes no sense to have this building for a tier 5 building.
suggestions for fortress: a very useful building imo would be something like reduce the iron cost for producing armor/weapons across the empire by % like the ironeers bonus, of course it would have to be high tier.
I would like to hear what people think of this, also dsraider, could you consider talking with davrovana and adding his tier 6 and tier 7 building thingy to this?, and possibly adding more buildings to tier 6?, that would be awesome.
Gonna put some thought into concrete suggestions for new buildings, thanks dsraider, cheers!.