Since im on Xbox i'll have to sit this out. My theory is that Reaper is an AI because of this line from Goodfellow:"Everything's in place" Goodfellow says this because Reaper is now fully combat ready, think about it the first 5 levels where teaching Reaper about fighting. ill give you a rundown:
Mission 1: basic air-to-air
Mission 2: data links
Mission 3: air-to-ground
Mission 4&5: practice them all at once
Now an AI of who you ask? well Mobius 1 of course! You can thank Camilla for that one by saying this in Mission 7: "Ribbion?"
that's my theory