One of the most obvious changes is the inclusion of pilots.
Before any craft can be used, pilots must be assigned to them (even interceptors). You can use any of the agents in the base, and their skills will affect the outcome of the combat.
A big implication of this is that you must have agents (and therefore living quarters) in all your bases, even those that you are only going to use to house fighters. Another, is that if all your agents are in a mission, or wounded, there won’t be any left to pilot your fighters.
The pilot’s skills affect their combat efficiency based on their Bravery, Accuracy, and Reactions.
Bravery <=30, slow approach, >=60, fast approach.
Accuracy bonus for pilots with accuracy over 55, penalty if below.
Dodge bonus for pilots with reactions over 55, penalty if below.
Their stats also improve after each combat (at random), and this might be the best way to improve an agent’s Bravery and Reactions.
If the craft is shot down by a UFO, pilots and passengers are still able to eject. If they survive (about 3 out of 4 times), they’ll return to the base after some hours.