Near me 14 of the 22 for sale new are manual with most being GTs but several V6s. When I was buying in December most were autos. I'm not sure one would be better than the other at trade in. Private sale possibly the manual if someone is looking for a fun weekend car but fewer and fewer people drive stick. I agree with those above that you should just get what you want. They sell so many no matter what you get there will be plenty of others for people to chose from you'd have a hard time getting a premium.
I don't think Nav would be a deal breaker for someone buying a used muscle car so I'd only get it if you want it (I didn't but did in my Jeep). If I were ordering I would get the back up camera and Brembos. While the recaros look awesome I'd get the comfort package so you can drive it in the cold (I didn't have it in my Challenger and driving in Oct/Nov before it was put away for winter it was cold and annoying). Best of luck.
2014 GT Premium, Sterling Grey, 6 Speed, 3:55 Gears, Comfort Group, GT500 AB, 3dCarbon Spoiler, JLT CC, Boss 302 Alcantara steering wheel, FRPP TrackCal, FRPP Brembos, FRPP Wheels