i have pretty much found specialist cities to be a complete and total farce....
as soon as you start to really specialize a city , you start gimping it in other factors. whatgood is a super science city that does not have the hammers to build a library? also , there tends to be few buildings that truely allow for specialization to the extent to make it worth while.
there are 3 types of specialist cities that people talk about....
1- science , here your looking for maximum TRADE potential and maximum BEAKER potential. you have several sources of raw BEAKERS (elder council , alchemist lab? , temple of the veil , stigmata of the unborn , catacomb librarus , and great sages). then you have several sources of modifiers in terms of percentages ( library , crown , academy , asylum ). as you can see its not really all that much for pure BEAKER production or modifiers. if your looking to go this route i highly suggest going with the AV religion and having as many cities as possible (your passive research alone is massive).
2- income , here your in a very similar sitchuation as i describe above , however you have many more buildings that give you percentage modifiers to your income.one thing to ALWAYS remember , these modifiers do NOT alter TRADE amounts but only the amount of GOLD earned. in realism you have only a few things again that give you GOLD ( market , gambling house , temples of kilmorph or order , great merchant and great priest ).
3- GPP farm cities. here you see ALOT of people depending on the wonder for 100% bonus and typically want to put one of 3 wonders depending on how you desire to farm GPP. the 3 wonders are (alter , crown , or bazaar ). these cities are often highly gimped due to thier necessity to maintain ALOT of farmland and the dedication to dealing with happy and healthy issues in the city. basically if you see an opponent with a city with massive amounts of farms .... burn it ...
now for the part that ALOT of people miss from the game ... TRADE..
the coins you see generated on tile plots are actually trade points and they can be split between research , gold , or culture. your second source of trade is from trader routes. each city has a base of 1 trade route available and it requires either another city of yours to trade with or open borders with a civ that you have established trade contacts with (the little triangle of arrrows).
the farther away the city that your trading , the larger , and wether it is foregn or not effect the base number for this. there are also many buildings in the game that add to the number of trade routes and the income they produce.
the benefits of expansion ....
as you build more cities yes your cost will increase , thats for another day and another chapter. however , every city you build increases your income by providing another source of trade routes. it also will provide a gold or beaker bonus if you have a holy city.
summary,
its possible , easily , to have each of your smaller cities to gain trade routes that are available for use as research or gold quickly and easily. I can often get my total trade route yeild up to the 30-40 line per city. this basically simulates having 6-8 towns that cannot be pillaged or disputed with. preplanning how to deal with many smaller cities and maintaining a false cap of lets say "9" on a city (aka only working the effective first ring) will allow for each of your cities to produce a few specialist and provide a large amount of trade.