There is never a shortage of people who discount or scorn theory, but in the end if it wasn't for wave theory you wouldn't be reading this on the internet, without newton's theory we never would have sent a man to space, and if it wasn't for sending a man to space OR atomic theory, you wouldn't have a flippin' computer running on polysilicon transistors 9 angstroms thick and 22 nanometers long to play Civ V on.
Wave "theory" and Newton's "theory" are fundamentally different from the "theory" that's going on in this thread because "theory" means something different in science. A theory in science is something that is generally accepted as true, which has a solid mathematical backing and good experimental evidence. The theories put forth here are not "theories" in the scientific sense, they're hypotheses because they haven't been tested yet.
I'm not trying to discount the value of theoretical thinking. It's definitely very important, but what many people here are contesting is the notion that having a convincing theory (or "hypothesis" if you prefer) means that you're indisputably right. You never accept something on the basis of theorizing alone--nor on experiment alone, for that matter. You need both. Although the theorycrafting going on here provides a good approximation, it would be naive to assume that the complexity of Civ can be modeled by a simple math equation. There's a whole bunch of factors in play that mean that theorycrafting like this is never 100% correct, which is why it's necessary to test these things in a game to make sure there isn't some critical variable you've forgotten, or some miscalculation you've made.
On to my own opinion on the matter: I definitely think Order is better for science and SV. Why:
1. Worker's Faculties gives a significant science boost from factories and lets you put them up faster. While 25% isn't actually 25% due to previous modifiers, it's still going to net you at least a 10% boost to that city's science output, something that Freedom doesn't really have.
2. It's still possible to run specialists with Order. Freedom gives food, happy and hammers (with StoL) from specialists. It's been said before, but that food is maybe going to get you one extra citizen per city by the end of the game. That's likely not going to end up being near a 10% boost to science, especially since the factory science bonus will come a lot earlier. With happiness, you just need to make sure you stay above 0 to get the bonus from Rationalism, which shouldn't be a problem with all the happiness policies in Order. Then there's hammers, which is nice but won't vastly increase your science output, and Five-Year Plan can partially replicate that hammer bonus.
3. Spaceflight Pioneers gives a free GS that Freedom doesn't get, meaning you can push through techs faster. The free GE can be used to rush that last spaceship parts, and the previous ones probably won't be delayed *that* much by the inability to gold-purchase, surely not by more than the 8 turns that the GS will save.
That said, this is just theorycrafting unbacked by actual gameplay, so it must as always be taken with a grain of salt.
Freedom has its merits, sure, but in my opinion Order will probably win out here. Actually, it seems like Order is stronger than Freedom in general. Anyone else notice this?