Your pilots will learn UFO flight patterns and weaknesses, therefore they will become much better at shooting down alien craft: sortie experience provides +3% to hit per kill (up to + 30%) and +1% damage per kill (with no top limit). UFO kills will grant experience to your pilots and provide a bonus to accuracy. You will need to cycle your craft regularly like your soldiers.
Along with that, your crafts and armaments are significantly less potent, at least at first.
UFOs are tougher, faster, and much deadlier in Long War.
