Wonders are one cure for the more...more syndrome, but rather expensive.
Choices are limited, but you can also influence what buildings are chosen by the Shift+A trick. These are general tendencies and don't work for every city.
If you want a trade multiplier, put your people on the ocean for more trade. You will get marketplace, library, bank, university in that order. (May not work if you can't reach enough ocean but definitely works if you have gold.)
For aqueduct go for the grasslands and rivers for more food. You have a better chance of selecting aqueduct as your population approaches 10.
For factory, go for the mined hills and forests. (Shift+A never selects mfg plant)
For barracks, take every citizen off the land. Two exceptions to this. If you have trade routes, you will get a trade multiplier. If city population is 12 or greater, you will get city walls.
For any of the above suggestions, you can naturally put your people back where they belong once you have your selection. Nothing is binding until you go into city check.
If you want a temple, cathedral or colosseum, you have to let the city go into civil disorder for one city check. For me, this is never worth it.
The bottom line is, once you have all the tech, you need to take 10 selections off the building menu for it to be displayed. Every wonder built by anyone takes one selection from every city menu. Not being on or next to river or mountain removes the hydro plant. Hoover Dam has the side effect of eliminating the nuc plant and hydro plant selections (on one continent).
Also note that marketplace and bank together only eliminate one selection. Same goes for library and university.