Hey Toob - Just looking at your screenshots above and your description, that does look really pretty bad. As GPH mentioned, you need to get improvements up asap. Here's some major issues as I see them:
1) Athens - I'm not sure of the RNG start generator on Vanilla but it appears that you may have moved your settler into a bad position. Only 1 hill in the BFC and all those sea tiles from the lake. Not sure what your thinking here was, but having not seen seafood I would be inclined to, if I moved my settler, to move it into a better position to balance food and hammers.
2) I think you may have overlooked parts in strategy articles about city specialization. Look to setup commerce cities (cottages), production cities(food/hammers) and a GP farm (food). The capitol is often a hybrid Bureau cap with lots of cottages if the land permits, not always though.
3) The lack of improvements in AThens and elsewhere just can't happen. Decide what you want and make it happen asap. Get the food specials up first, then other specials/strat resource, mines and then decide if you are going to cottage up for Bureau or just go straight production. Sometimes the cap start is such high food that you make your GP farm eventually and move the cap to a better bureau site.
4) The lack of improvements seem to be a combination of poor overall decisions and lack of workers. However, I see a copious amount of unnecessary roads. All you need is to link up your cities with a road for trade routes, but workers should be focused early on getting tile improvements up and chopping. Later, once workers have less to do they can go around building roads everywhere.
5)
but I know I'll want to watermill those tiles asap
This statement doesn't make much sense. Basically you are saying to get up watermills asap, but they don't come around until Machinery. Watermills are a fine improvement in the right cities and with the right tech (Replaceable Parts, Communism), but not improving your land in expectation of a later tech is not good. Farm or cottage those tiles depending on the city time. Decide later if you are going to turn a city into a workshop/watermill/windmill hammer paradise later, but get the bonus you can get now -- ASAP. I would not bulldoze developed cottage cities though unless doing so late for the space race to build parts faster, but you need the commerce early to get to those part techs.
5) City placement. Unless you are Creative, you need to settle your cities near specials, especially food to get them up and running quickly. Besides settling what appears to be fairly poor land in the first place, I notice that most of your cities are settled such that they have no specials in the first ring of your BFC. This means that you have to slow wait for your Monument to build and then 10 turns before you can even improve a good food or hammer tile. These cities are basically useless and not contributing for 100 of years.
6) Spart is okay, but it seems you may have settled in the wrong direction. Hard for me to say since I don't know what the mapped/scouting look like early. Block of some good land toward the AI and seal of land to your back which you can backfill later. Or get up 2 or 3 good cities and go out and conquer some better land.
7) Teching Alpha at 900AD is a bit odd. If you don't tech Alpha directly it is something you should easily trade for much sooner than now. You want Alpha at some point fairly soon to start tech trading. I'm wondering here if you are trading techs at all. It is an important part of the game, although on lower levels you don't have to do it much once you get good enough at that level since you will start out-teching the AIs by quite a bit. Still, tech trading allows you to keep a focused research path based on your strategy and then backfill some of the overlooked early techs via tech trading.
7) Great People - Not sure of your use of them based on just the screenshots, but they are important. Get a library up asap, usually in your cap so that you can get your first Great Scientist for an academy, again usually placed in your cap. The academy will boost your research rate significantly. Later, find a good spot for a GP farm city. A high food city where you put the National Epic and use it to pump Great People. Specialist building go here, but you can also get out a lot of them by running Caste for a bit mid-game - even starving the city a bit to pump out Great People faster. This can set up some key tech bulbs in the mid-game to provide you an advantage. (Note: BTS adds a lot of new features, one of which is no-anarchy civic switches and GPP boost during a golden age, which is a great time to run Caste System and pump GPs)
8) A very important tech that you generally want to bee-line or trade for fairly early is Currency. IMO the most important tech in the game. It immediate boosts trade route income, allows gold trade for techs and resources, and allows you to build wealth to fund expansion, research and/or warfare. Make sure you are trading extra resources for gold per turn. I even trade some single resources if I don't need them. For instance, trade copper if you have iron or trade health resources if you are Expansive. The extra gold means extra research.
The most important point though that you need to take now is that you need to have more workers and you need to improve your land. Do not work unimproved tiles and do not automate your workers.