@eldar,
Not knowing for sure where the difficulties you experience reside, I can make a couple of guesses....
Technology costs in the MA increase dramatically. The cheapest AA tech is Pottery @60 beakers. The most expensive is Republic @720. The corresponding numbers for the Middle Ages are 960 and 2040. So self research takes more money. The AI trade rate at Emperor also becomes more of a factor...their discount for trading techs among themselves and the premium paid by the player become absolutely greater, making tech purchase more costly.
Villlages are growing into towns and towns into cities so contentment costs more.
To support either self-research or purchases of technology and to keep the population happy, commercial improvements are critical. That means courthouses and marketplaces everywhere. Most players look at the marketplace for its happiness benefit and some don't build them unless they have two or more luxuries. But the commercial benefit is even greater. Courthouses also have an impact on contentment as saving even one more gold piece from corruption will make a citizen content if there is any luxury spending at all. Harbors also help in coastal cities as you get 2f2g without any worker turns.
A shortage of workers is also a problem as it directly affects commerce and productivity. Judging from the last save we are short workers.
So Doc Bede would prescribe courthouses, marketplaces and workers, libraries if we can afford them, and temples only if you can't think of a better use for the shields....and there is always a better use. (vipr can recite the temple rant)
DocT, scout, comments or brickbats?