Voice - i guess your big on hered. rule. Why, when rep helps science so much more?
Ok, by 1000 BC, give a recap. What should I have? (ie, how many cities, what buildings in each, civics, etc...)
dannyusmc78,
It sounds like you're looking at a specialist economy, but only dipping your big toe in instead of jumping in. With that, I say that you should dive right in. Look around the forums, doing a search for "Specialist Economy" will yield tons of threads that give detailed results. Then play a game or two. Your first game will not be the best game, in fact, expect to lose.
With that said, you need to specialize each city individually.
If you have a non-coastal city with no river access and lots of plains and hills, with no silver/gold, etc. this city will be putting out virtually no commerce. No commerce translates into no research. So 25% of 12 beakers is 3 beakers. Do you really need to spend all those hammers to generate 3 extra beakers? And 50% of 12 beakers is 6 beakers. A settled Great Scientist generates 6 beakers (+3 with rep) and 1 production...which is multiplied by other percent modifiers (library, university, academy, oxford, etc.) This theoretical non-coastal city with no river access should be your military production city. Build a barracks and pump out as many military units as you can afford.
Now the coastal city on a river with fish, corn plains, and a gold mine is where you want your commerce city to be. Commerce means research. Now if land is tight, perhaps you need to build a University in your military city to get the X Universities necessary to build the Oxford University, but hopefully this isn't the case, and this should be one of the only exceptions to building anything other than military units in your military city.
Regardless of which economy you choose, you don't need a barracks in a city that won't product a single military unit, and you don't need a library in a city that won't produce much science. (There are exceptions to both rules, of course.) Always think about what this city would be good at producing before building the city.
If you're building a city to gather resources, ask yourself "When will I need this/these resources? Now, Soon, or Later?" (In the 1st, 2nd, and 3rd ring? - The 3rd ring is an unworkable ring.) If you won't need the resource for a long time, you have many more placements, because you can position your city so that the resource is in the 3rd ring. Thus you can ask yourself "What do I want this city producing?" If you want that city producing great people, position the city so it gets access to the most food. If you want that city producing military units, position the city so that it has access to the most hammers.
The key to winning later difficulties, specialists or otherwise, is making every piece of food, every hammer, and every unit of commerce count. Hammers that go towards a Library that will eventually generate an extra 2 science a turn is wasteful. Where as hammers that go towards a Library that will generate an extra 25 science a turn is efficient.
My advice to you, dannyusmc78, is to play a full blown Specialist Economy game. Once you get that down, try a Hybrid economy. I love Specialist Economies, but I tend to have problems during the end-game because I run with 5 or fewer cities. Where as Cottage Economies tend to do very well end-game, even with only a few cities, because of all the bonus commerce that towns produce.
Regardless, good luck, and have fun!
