As a member of the Vanu Sovereignty, I know that the Scythe has a speed-boosting ability, but it looks like the TR Mosquito has landing gear or something, which I don't seem to have. What's that do? I assume that the NC has a third?
Short answer: No.
Longer answer: All Empire-Specific Fighter aircraft (Scythe, Mosquito and Reaver) start with the same basic afterburner ability. The acceleration and top speed this ability can achieve vary between specific fighters and can be altered by that aircraft's Performance certifications.
If the pilot has invested points into the appropriate Utility Slot certifications, they may also be able to equip additional abilities, such as the Scout Radar (nearby enemies shown on map), Decoy Flares (disrupts missile lock-on attempts), Ejection System (pilots can bail out safely) and Fire Suppression System (removes the effects of critical damage). The abilities are the same across all factions.
Other abilities are also available in the Defense Slot category, such as Composite Armor, Nanite Auto Repair System and Vehicle Stealth. These are passive systems that do not need to be activated.
Simply put, each empire/faction has a special characteristic:
In battle these advantages are not very prominent, but they can make a big difference.