Newbie....
I've got my space plane flying around via player keyboard input using 3rdpersonscontroller.
From my AI scripts how should I "AI control" my non-player game objects?
Do I maintain direct control using transform.rotate, etc?
Or do I fake keyboard input?
Whats the suggested method to control orientation and speed from my AI scripts?
Suggested method... None.
AI can be done in a huge number of ways, if it is easier to control it directly by modifying position/rotation, do that. Or if you already have a working script for processing user input and controlling your unit, you might want to fake keyboard input to avoid having to write everything again for the AI, also you get a bonus that the AI will never be able to do things which the player can't.
There is no "Best method", go with what is easiest for you/you think will give the best results.