i dotn see the need for speciailization. why specialist at all? if.. say the AI gets smart enough aand captures every production and military cities what do you have left? youd have to change your GP and cottage cities into military powerhouses and that takes time.
and build every building, thus if even my capital ( always the core research, financial and production city) is captured and/or razed i can still carry on without changing a thing. usually i set up my second city to be the second most productive, etc city.
It sounds to me that your game isn't all that stable, yet. Especially when you say something like this:
and besides, the only city that is half decent or better is the capital, all other cities just plain suck, in any era.
The reason your cities suck is because you don't specialize them.
The principle is quite simple: Cities have the potential to benefit your Civ in different ways. The first one is coastal, the second one is ripe with

resources, the third one is mostly hills and forests, and the fourth one has bonuses for both

and

. For an example. Surely there are more or less efficient ways of managing your resources and your population?
The coastal city would focus on

, the second one could be used to run specialists (a good way to create

, which is a good idea in itself), the third one is a solid weapons forge and the fourth could be a combination of money and production (perhaps for building Wonders). Building

buildings in the coastal city would be less efficient than building

buildings. And building

buildings would be most useful in the first and the fourth city. If you build your units in the third city you don't need to build Barracks and Stables in the other ones. An so on.
It doesn't, of course, hurt to have
all buildings in
all cities but its wasteful when you could only build say 1/3 the number of available buildings in any given city and only perhaps lose 1/10 of the potential benefits. The rest of all that production could go into building World Wonders - and units. That way you're not constantly under the threat of imminent destruction by warmongering rivals.
Sure, eventually you would wanna build all the

and

buildings in all of your cities (to keep up with costs and not to be outproduced by your enemies), but only after you've taken care of the
priorities. At the very least, you should build all the buildings in the order that they do the most good to the city in question.
You do however have a point in building a more solid empire, where no city is more valuable than another. But this could just as easily count for the
rest of your empire, aside from your
core cities.
Personally I tend to focus on a few heavily specialized cities for my

, maybe one dedicated

city and a handful of

cities to get out the units. The rest of my empire is there mostly to cover territory and grab resources. These cities tend not to be as important or useful, and end up being either dedicated

cities or supplemental

suppliers. Because by that point I will be needing both units and cash to maintain my empire... There is little point in, say, building the more expensive

buildings in these cities, as all of them wouldn't amount to even one of the specialized

cities (with Academies and specialists).