Please simplify the science/education upgrade.
yes, i'm not fully content with them either.
Monasteries should be considered part of the religious upgrade, and yes, I think it's fair that they still produce science. I would recommend something like this:
monasteries still produce science. note that 3

~4

when you calculate in all the commerce and science modifiers. commerce is just more general and usually better then pure science. it only looks a bit confusing that it's a coin.
Elder Council => School of Scribes => Library=>university (req. 3 libraries) OR academy (3 libraries)
that was my original intention anyway. but one thing is that libraries are no education sites per se. at the other hand monasteries belong exactly into the chain of education buildings - at least from an european/christian point of view. this is why i finally decided for the historically correct path.
Library (PRE-REQ, not upgrade) => Merchant School => Public School
i think i will drop the merchant school and gymnasium for the next version. instead i will make monasteries upgrade to either schools or universities.
Reduce Academies to +15%

-10%
sounds reasonable. however when the gymnasiums drops out the building prerequisite will need to change. the original idea was to either decide for a classical education system with the gynmasia/academies or go for monasteries. having both combined in one city would cause a research overproduction.
trade route buildings:
Please change back River Regulation; it's pointless to build the Pyramids if all it does it give you River Regulations...The Pyramids are supposed to be representative of Egypt's ability to manage it's food...that's why it was originally granary and then irrigation canals.
hmm... well for the sake of the wonder i could reintroduce the irrigation canals but make them not buildable. thus you only will be able to get them if you build the pyramids. otherwise rivers became too overpowered again as they got a total bonus of +1

+1

+2

and that was too much.
city trade buildings:
Moneylender => Bank => Investment Bank These should have no unhappiness modifier except with certain civics (e.g., Corporatist, Guilds)
i actually like it that way i find it historically very fitting. and since financial buildings did not give any bad effects unlike other relevant buildings that give

or maintenance. well, but if i get more complains about it i will move the unhappiness penalty.
religion buildings:
- Sanctuary => Temples (and Monastery) => Cathedrals => Religion specific Wonders
- monastery: Pre-Req Temple of that religion. Does not replace or upgrade to anything else. +3
+2
+2
+ religion specific boni
here is the problem again. monasteries don't fit into this chain due to their very different nature. temples and cathedrals are places for religious worshipping while monasteries are sites of education and study of theology but also philosophy and mathematics among others. and while temples and cathedrals are always in the middle of settlements monasteries were mostly build far beyond the cities wall. in fact they were self sufficient and were like small towns themselves. and as i noted before: the oxford university was originally a monastery.
about science and education buildings:
Recommend that Gymnasium be moved as a Greek-Specific Building, and not part of any of the other upgrade changes.
as i said i will most probably drop the building.
And, of course, I strongly disagree with the banking issue from both a gameplay, historic, and balance perspective
as i said. historically banking was associated with usury among the common and simple people. and since most of the population are peasants you can expect quite some unhappiness due to this. the few merchants who understand how important banking is won't compensate the broad unhappiness of the poorer people. and as for an explicit example: look at many peasants of today india. they hardly can compete with the modern food industry. they lend money to buy some better more resistant seeds and maybe some pesticides but in the end they can't pay their debts back and many choose the simplest escape through suicide while the banks get their land.
but... if there are more people who dislike that, i'll change it.