The interesting, age-old discussion of what the purpose of the S-Foil could actually serve... Hopefully such a late post in the discussion won't bother anyone...
This site in my opinion is the best reference to the X-Wing I've ever seen:
http://saxman.xwlegacy.net/You'll need to find the link to the X-Wing, of course, but the author has "done his research" so-to-say (via novels, the films, etc.).
In terms of maneuverability, the operation of the S-Foils might warrent slightly different handling characteristics. As mentioned in the article above, the closed position of the foils yields a slightly greater "thrust footprint" to the lateral portion of the craft. Given that the fighter has some degree of thrust vectoring or differential thrust (any ship like this would require it... heck, even the Y-Wing has thrust vectoring!), this would enable slightly greater yaw authority. This would not be much, but there you go.
When the foils are opened, the engines separate to a much greater extent above and below the center of mass on the xy or yz-plane, thus enabling greater pitch authority via a greater moment. If we are to believe thruster banks are installed on the trailing edge of the foils, then this would also serve to improve pitch authority when the the foils were opened in the sense that the thrusters might be able to act in a similar manner as differential thrust in the engines as described in the scenario above. Thus, overall maneuverability is greater when the foils are opened, as everyone should figure naturally. Supposedly this act also increases the effectiveness of the deflector shields by augmenting their coverage area.
In terms of gameplay, implementing S-Foils would require a shifting of table values for the X-Wing when the system was engaged. How the table shifting could be done, I have no idea. However, as someone already suggested, this transitional prompt would most effectively be done by using a "primary weapon" called "safe" or something like that. The next part would involve making sure only one primary weapon could EVER be selected at one time. This would serve the dual function of disarming the cannons when the S-Foils were engaged ("safe") as well as actually moving the physical wings/shifting flight model tables. Obviously, this process would go both ways. Also, entering subspace/hyperspace/somethingspace would need to cause the S-Foils to close as well.
If the argument is attempted that closing the foils has some sort of performance boost, it is mostly out of the scope of FotG UNLESS you make an argument for a specific case, which I will cover shortly. If there were atmospheric missions, closing the foils could indeed bring about a greater sustainable speed. The X-Wing obviously does not really have good aerodynamics. However, with the foils open, the aerodynamics become worse at speed. This would be due to the fact that a great deal of airflow is trundling about between the split wing surface (making the S-Foils act a little like an airbrake). For the Rogue Squadron games, this is acceptable as a game dynamic as most missions took place in an atmosphere. In the case of FotG however, what could be argued is that closing the foils disarms the cannons and thus means an automatic transfer of power from the weapon energy to both shields and engines. This change would be gradual in actually occuring, and would be likewise in reversing. Thus it might take a minute for the effects to be realized. This would mean that the pilot would have to coose well when he/she would employ the foils, thus denying any stupid "gamey" trick in simulation. The application of the foils could be as follows: (1.) on a patrol, you want to move through waypoints faster. Thus you close the foils. Also works great for triggers/ mission situations. (2.) entering the hangar and landing perhaps. Diaspora will have landing ops. It would be really cool to see Fate of the Galaxy have this as well. Heck, even TBP had recoveries aboard a vessel to an extent.
Of course, this is all just brainstorming and speculation. I have faith in the experts to develop something worthwhile

-Thaeris