I think wonders reducing the cost of research buildings would be a fine idea, but with some provisos.
It occurred to me that possibly the reason that I (and possibly Joseph II as well?) am struggling with this and some of these wonders are causing quite so much of an issue is because of my playstyle, those arguing that this is not much of an issue just simply do not prefer to play the game in the way that I enjoy best and don't realise the issues that it causes some of us!
I am very expansive and enjoy the game most when I've set it up almost so that I am in sandbox mode (and the thing I hated most in CIV 5 besides its lack of depth, was that it did just not allow for this, and was aimed more at a smaller centralised empire with a strong military component to the game - just look at the requirements of some of the national wonders that required a certain building in every city, that's just not ever attainable if you keep building more cities - anyway, I digress).
I end up with many small cities, and I play with civic city limits off, because for me most of the fun is in having lots of cities. Once I have a second or third city founded after tribalism, I always have at least one city building a settler unit (and sometimes multiple cities pumping out "new city packs"), right throughout the game. I do not have loads of spare cash. I have few AI civs on a gigantic map, and I try to take most of them out and take their cities (and get their base cultures through assimilation) early on. I leave a couple that are in out of the way spots, but my ideal is to have a large empty map to expand into. Yes, there are lots of different ways to play CIV, this is one of the ways I enjoy it most, a sandbox freestyle type of play.
In my current game I have not yet researched writing, but I hit the Classical era from the glass blowing tech. I have 19 cities. I have the pre-writing tech research buildings in every city, loads of myth buildings. My income is not at all good because I'm paying a lot in city maintenance and city distance maintenance (I captured and kept a couple of cities from other civs all the way over the other side of the Eurasian type landmass on a gigantic Terra map).
Once I hit writing I am going to enter a dark age, because most of those free research buildings/myths will obsolete and changing civics to interpreters/written tradition will not make up the shortfall. Even though I could build the Kemetism temple religious wonder to give me a school of scribes in every city which would set me up OK again in terms of beakers, there is no way I can afford the cost of a school of scribes in 19 cities - because it's not the same as using the research slider which I can do in 5% degrees, it's all or nothing, I can't build it without destroying myself.
The way it is currently favours smaller empires with bigger cities, a more expansive "sandbox" mode is hugely difficult (because every time you found a new city it gets whichever -gold building you built the wonder to provide, but without any beaker production to provide any benefit, thus effectively preventing expansive play), and it is a mode of play that was always viable in vanilla Civ IV/BTS or ROM/AND, and C2C up until recently!, so I don't like that it's now become so difficult! And I do not want to lose the fun that I have, playing the way that I like to play it, to be forced into a different playstyle.
Onto something a bit more constructive!
I have a proposal. Introduce some National Wonders that will balance things better for those who prefer to play a more expansive game, but won't be relevant for those who keep things smaller and more centralised.
Example: (Insert appropriate name here, something like "national scroll repository"), National Wonder. Available at Writing, Obsoletes with Printing Press. Requires School of Scribes, requires scrolls or tablets. Requires: civ must have more than 15 cities.. Benefit - halves cost of school of scribes in all cities in your civ.
Similar thing for libraries, using the same techs as library for available and obsolete, requires that your civ must have more than 30 cities (or possibly higher). And so on for more advanced research buildings.
It would put the fun back into playing an expansive "sandboxy" type game, and probably not affect those who prefer a smaller, more concentrated civ, so don't have their economy suddenly go down the tubes because they built a wonder that turned out to be more of a hindrance than a help. In fact if someone can point me in the direction of a tutorial on how to make and add wonders, I'll even try to do it myself, to see if it works for me and for the few other people who like to play in a similar way who are finding things difficult right now!
Thanks for commenting. (Although as a dyed in the wool leftie, I am not sure about your pendulum comment 
on a library as the cost that is required to run the library but why should having a bank in the city increase that?
gold
) Then let Epona, me, and others like us play with it for a bit. If it's workable we'll tell you. If there is an underlying problem still we'll let you know that too. 
