For me, usually just after they beam back aboard, one of their systems go down, typically engines... I haven't been using it much except for battle cruisers when I have been solo-ing... but I like it more because of the coolness factor that you mentioned...
Yup, coolness factor wins for me. I could easily see temporary ship-takeover though. It would effectively behave like the science ability (Scramble sensors I think) - and it temporarily shifts the ship to 'your side'. I hate to give it up but the whole taking over of a ship might be too much.
Hmm... except - I can see if a ship is at 0 crew, but still has hull left, you gain control of it - but only as a pet / dumbfire kinda thing. It would follow you like a shuttle pet, and maybe shoot a single weapon at your target occationally. That would be very cool looking!
or you simply capture it .. and you can refit it and fly it yourself. having extra AI flying with you might load the servers even more. having an AI fleet flying with you will probably be a matter of 2-3 years from now ... if ever.