Shifting science cities - from specialist to cottage

In the game I'm playing now, I stayed with just my capital for a while, and I have five religions built there. I've also built monestaries for most of the religions. It has access to 5 seafood specials, and some room for farms, so it seems like a good place to raise specialists.

It seems to me, though, that it'll make sense in the course of the game to convert this into a financial/gp farm, and make another city the science city. In fact, since so many science benefits are lost somewhere in the middle ages, it seems like it generally might be a good idea to do this shift.

Here are some of the ideal aspects for both cities:

Old Science City:
Located on coast, hopefully to benefit from Colossus and Great Lighthouse
Lots of food, including seafood and farms
Specialists (at first scientists, shifting to priests/merchants later)
Great Library, as many shrines as possible
First Academy, National Epic, (later, Wall Street)
Library, monestaries (later, market, grocer, bank)

New Science City:
Located inland
Ideally has a river through it, maybe with a food special or a floodplains for growth and a few specialists eventually
Cottages everywhere
Second Academy, Oxford
Library, University, Obervatory, Lab

2 academies instead of one isn't always the best move

There are 2 different situations :
1 ) going for early domination or cultural or diplo.
The GL won't obsolete (at least not until it doesn't matter anymore). So the best place for oxford is the GL place. corporation is nowhere near most of the time, so wall street won't happen.
2) going for late game domination or time or space
Maybe you'd be better off building the GL in another city. 5 potential shrines is cool, and Wall Street will be great. But you don't need the NE there.
Better to have NE and GL in city n°2 and build oxford there too.

Well, in the context of my game (I'm thinking in terms of long game) I have the choice of trying to build the Great Library in my capital, where I have a population of about 15, a good bit of hammers, and the ability to rush through slavery - or in a city I just captured that has a pop of about 5 and very few hammers (I picked it for its potential for cottages). I just don't know that I'll have the hammers to build it and all the other stuff I'll want there (library, aqueduct, university, colloseum, etc.)

Also, the GL is going to be obsolete for the free specialists pretty soon, and I'd like to have those magnified by the existing monestaries I have in the old city. After it's obsolete, it will still generate GP points, and I'd like to have those in my GP farm.

I also think I'd want the National Epic in my major GP farm / Specialist city.

On the Academies, I will typically build more than one academy, even when I've stayed with the same major science city. Although, it may be better just to build the academy in the new city, and use any later great scientists as planted superspecialists in the new city.

A lot of this changes when you're playing a civ that's not spiritual, so that you only get religions in non-capital cities. In those cases my capital usually ends up being my science city all through the game, and I might try to make a city where a religion shows up as a financial/religion/GP city.

major difference is that i usually settle a prodution city as second city...
different playing style obviously

I wouldn't recommend making your capitol your GP farm. GP farms are best with farms/food, while your capitol wants cottages for commerce/Bureaucracy.

I do agree with making your capitol a commerce city. Not as a gold/finance city per se, though certainly you won't be remiss building Wall Street there with all those Shrines. The degree to which your capitol is either a research or a gold city is determined by your slider.

If, however, you never plan to run Bureaucracy and you don't mind having a merchant GP farm, then forget everything I said so far. Your capitol will be great.

Switching my "science city" is something I do myself in many games. However, I don't usually put an Academy in the early one. Only in the latter one (the one that gets Oxford). Having the latter one be my GP farm is often a good idea. You can run tons of scientists, and your science won't be tied to the slider (so if you have to drop down because of overexpansion or wars, you still have your top science city pouring in the research).

Anyway, early scientists I often use to lightbulb, rather than make an early Academy.

Wodan

Don't forget you can move your capital. In your situation that would let you run bureaucracy in a commerce city later and get the benefit of 50% commerce. And since your capital is coastal that will probably help with maintenance too.

I agree with your original plan - your capital should be an awesome GP farm. I would build an academy too - with a GP farm this early you should get a good number of early scientists and it really boosts your research.

I played a game very similar to this with Ramses on Emperor. My economy went something like this:

Early - capital had GP farm - build pyramids, built academy and settled scientists in capital.

Mid - had a mix of commerce and specialists cities. Made my best commerce city my capital to run Bureaucracy.

Later - ended up building Oxford in my capital - let me run even more specialists and also I had enough settled scientists at that point that they generated significant science. Having access to the pyramids early probably affected my play there - without that I probably would have put oxford in my new capital. (which also got an academy). All my specialist cities except for the capital got switched to building cottages with emancipation - I transitioned from a specialist heavy economy->mixed->mainly cottage economy.