The hybrid economy that I run tends to be far more complicated, than just ce/se. Sure cottages and specialists, are a very important part of an economy, but so many other factors tend to come into play.
1) food/infastructure/diplomacy, sure having 1 gold trade routes between your cities is nice, but imagine having huge revenue 5-9 gold each in all your cities, its a big help.
2) Not only relying on specialists/cottages for research, production cities should be turned to research/gold at times, this boost will help a lot(warlords only). Mfg determines the outcomes of wars, why not use your mines for research some of time.
3) Several amazing tricks/possibly exploits can also help you greatly in the early game. So you've overexpanded, dont have alphabet/currency and have massive production, are industrious, and have access to stone or marble. Build wonders but dont finish them. For example, with industrious/stone pyramids cost only a fraction of the 1500 gold=1500 research you gain from nearly completing, then stopping construction. Do this in multiple cities, micromanaging to negate decay, and you can then use dave chapell's saying " Im rich !". Using multiple cities with this tactic on multiple wonders you find useless, hugely efficient research can take place from the most unlikely sites.
4) Selling resources using the resource subsidy method is a great way to make some early cash (after currency).
5)When obtaining specialists early consider the value of settling them(especially on marathon). Do the math and you will find that their lightbulb is far less valueable than their aggregate contribution over the ages.
The most important thing to remember is micromanage then micromanage more, if every citizen of your empire meets his/her full potential, then the world will be in the palm of your hand.