I have a 66 Coupe (c code auto) and a 65 GT Fastback (4sp, pony interior, A/C).
I know you asked about ‘desirability, future resale and driving performance’ but if it was me, I would buy the one that has the least amount of rust, best panel gaps/fitment, best paint. Have you checked the fresh air vents for rust?
If the bodies are equal in their quaility, the choice is difficult. My Fastback is fun to drive, the body shape is great, the interior is cool with the blue/white pony trim and console. However, when I jump into the coupe, it is beautiful in its simplicity - standard black interior, no console, no A/C, no fancy back seat or rear window. The auto is fun also - kick it down, the tail digs in, the exhaust note is loud.
I've owned the coupe for 23 years and the fastaback for 8 - so I worked my way up the food chain.