Try a "trade economy" on an Archipelagos map (it works on other map types as well, but on Archi it's easiest). Spain is a good civ for this, but they all work well (you don't have to be Financial in any case). Portugal is another obvious choice for a civ.
In a trade economy, the bulk of your commerce will come from trade routes. They are totally zero maintenance (no cottages or micromanagement needed whatsoever), and get better and better with each new milestone tech.
The one thing you need is trading partners, so you should start exploring with Work Boats as early as possible to meet those other civs. Definitely don't wait until Optics with this.
Also, the Great Lighthouse is
really important, as it gives two extra trade routes to all your coastal cities, and chances are you won't build a single city which is NOT coastal.
You do not need the Temple of Artemis or the Colossus, but they are both very nice to have (obviously).
Your key technologies will be
- Sailing (for coastal trading and the Great Lighthouse)
- Compass (so you can build Harbors for +50% trade income)
- Currency (+1 trade route)
- Engineering (+1 trade route from the castle; Spain gets the citadel instead and can make terrifying siege weapons in those cities)
- Economics (customs house for +100% to most trade routes; this obsoletes the castle/citadel so might need to be delayed if you play as Spain for military reasons)
Basically you can go crazy with expansion, because most cities will be profitable at 60-70% science right off the bat, due to the instant trade income they generate. Build harbors in all cities.
Most of your trade routes will be "inter-continental", which gives a huge bonus by itself. More importantly, the Customs House (unlocked with Economics) gives another 100% bonus to these trade routes. You can imagine what this means in our case...
I have tried out this strategy lately on Monarch difficulty, and my GNP (commerce) was almost DOUBLE that of my next best rival for hundreds of years all the way into the Medieval Age. I did have a few cottages but their contribution was quite marginal.
While this was not advice on how to handle cottages, you can try it to see how to actually live without them (you seem to be locked in to a cottage spam strategy at the moment, which is why I'm offering this radical alternative).