Given that you run a hybrid what sort of map do you play and which victory conditions do you head for? How do you build an army? I am assuming that you will need to defend yourself against significant military threat even if you go for a peaceful victory. What other civics do you tend to run alongside Rep + FS?
If you think Hybrids are better what specific advantages do you think they have over either a CE or a SE played on the same map (depending on which type it favours most)? Do they give more research? More production? A quicker response to a military situation?
Map types etc... usually shuffle or fractal, normal or large - I aim for whatever victory conditions I feel like at the time. In my most recent game I was very peaceful - I was only in a few short wars (and only when I was declared on), and I only built 4 cities. I won a cultural victory in 1836AD. That was a normal size pangea map. But more typically I tend to conquer one of my neighbours and then use the land advantage to win peacefully (or continue on for domination/conquest if I want to finish quickly). I always play on emperor difficulty.
To build armies, early in the game... well I could go into the details about what I do but I don't think it is really relevant - surely it isn't possible to specialise to with CE or SE in the early game. There are essentially no civic choices, pretty much every city is restricted by happiness, you can't get enough specialists, the cottages haven't grown, etc. So late in the game, I typically have productivity centers that do most of the army building - these are cities that are completely dedicated to productivity. They'll have all the great generals, great wonders, and military national wonders. If I don't need the productivity, then I'll turn the miners into specialists.
For civics I almost always use representation. I typically use free speech - I only switch to nationhood if someone declares war on me when I'm not ready (or if I'm a spiritual leader I'll just switch at the start of a war regardless so that I can get a troop surge to win the war more comfortably). I'll use caste system if I can afford the happiness, emancipation if I can't. Free market if I can get a couple of good corps, state property if I can't (or rarely mercantilism if I don't have any good trading partners). The religious one depends a lot on the diplomatic situation, and on where or not I'm getting special bonuses from religious buildings and stuff like that.
About the happiness boost of nationhood. It's useful - but there are a lot of other ways to get happiness. I prefer the better cottages and better culture of free speech, unless it's war time. About drafting - it can be pretty useful, sure, but I'm not sure why you are bringing it up. It is equally useful for CE/SE/hybrid.
About the infrastructure for cottage cities - Most of those cities will have had their buildings whipped/chopped to completion back in the dark ages, but typically I'll let them have a mine or a workshop or something like that to give them the productivity if they need it. It's uncommon to have a city that has nothing but grassland around it anyway.
As for my perceived advantages of a hybrid. I think the main thing is flexibility. I figure that cottages produce better commerce per pop (and continue to give food), but only after a long time investment. It usually isn't work setting up new cottages late in the game, even with emancipation they just take too long to grow. Specialists don't need any tiles to work, their jobs can be chosen to suit the buildings in the city, and they are more easily moved to productivity if required. Oxford Uni, Wall Street, and of course National Epic are all most efficient in specialist cities. Cottage cities will often have a food resource or some farms anyway to help them grow to full size. Once they are fully grown, the extra citizens will be specialists. When a city has a lot of food resources, you don't have much choice but to use it to run a bunch of specialists. There is only a choice for cities that have lots of grassland.. and for those I'll run mostly cottages. If I capture a city that is surrounded by towns, I'll leave it that way; but if it just has a mishmash of improvements I'll turn it into either a specialist city or a productivity city, because those are faster to set up (even still, I'll leave any towns that it has around it unless I need the tile for irrigation).
-- ack. This post of mine is really long, and probably pretty boring as well. I just tried to answer all the questions. The short version is just what I said in my previous post: different cities are suited to different tasks. High food cities will have at least some specialists. Flat grassland will probably be better with cottages. Captured cities will have what they have. And I think that trying to fully specialise towards CE or SE will only give marginal benefits for the cities can do anyway, and will harm the cities that are less flexible.