Ok, somebody help me out here. I can't seem to figure out how an SE can work without pyramids. My problem is primarily that early game, before monarchy, I am severely happiness limited. 5 in my capital, 4 elsewhere. So, I build two grassland farms in secondary cities and run 2 scientist when at max pop for a grand total of 6 beakers, and 6 GP points. I can use slavery to whip out buildings and troops when I need to and quickly grow back. Or I can build 4 cottages and whip back down every 10 turns or build them on plains to limit my growth. My capitol is food rich and I make it my GP factory in a cottage economy. After 10 turns, I am bringing in 8 commerce at max pop from my non-capitol cities and this only grows with time. If I am financial, that is 4 more, and if the squares are river-side I get an additional 2 over the SE because I am working two more of the river squares. With the SE, even if you have a philosophical leader, you are not getting anything over 6 beakers
Early game GP points are very powerful. You get about 5 beakers to the GP point if you lightbulb IF you get a GP from them. But each GP costs more GP points and the benefits of the GPs don't scale linearly with the GP points required to make them. My problem is that most of these cities are never going to produce a GP. I have GP points saved up from all these different cities that are basically wasted. The way I see it, GP points are valuable in the city with National EPIC and lots of food but basically worthless in all the others. On immortal difficulty, I successfully ran an SE with pyramids early using Frederick. By the time any city other than my capitol started getting GPs, it was late game and they were not worth much...paying 6000 GP points for +1500 tech is not worth much. And you have to wait for those GP points you invested in 3000 BC to actually produce a great person in 1440 AD because that is when it finally catches up to your capitol which has National Epic and lots of food.
Without the GP points, the specialists in your satellite cities are far less valuable than simple cottages. So it seems to make more sense to build a SE in your capitol and cottage your satellites, but this doesn't work so well with beuarocracy later on. So maybe cottage your capitol and make your first settler go to a good location for specialist production. Then cottage everything else. If you build GPs everywhere, you will still only get GPs wherever you built the national epic in the early game, and late game, the specialists will be far less valuable and you have to wait a damn long time to reap the benefits of those GP points you invested in 3000BC.
I can't seem to get past 1000 BC running a SE on diety. This is simply because I get my great scientists at the same rate as with the cottage economy (early game, i.e. just the ones from my capitol), but I don't have nearly as many beakers and gold because 6 beakers <<14 commerce. By 1000 BC, I am so far behind on tech that I can't trade my way back in. They have every tech I can research.
Perhaps I am missing something, but I can't get this to work at ALL without pyramids. Even if I have happy resources, I simply don't have the beakers to keep up with a cottage economy or the diety AI.
But in many games I make a mistake here or there and I usually get discouraged when the research rate is far lower than the one I'd have in a cottage game, so playing the same map along with others going for a SE would definitely help me. 
There's a lot of "out of the box" thinking in US's Deity University thread. When I saw how far his first two settlers went.....wow.
payoff, which you can use to run deficit research.
