I wouldn't buy another truck without adaptive cruise. It seems gimmicky, but it's a game changer when you have long travel days.
I would go with crew cab for the additional storage space (even if you don't think you need it) and resale.
I'd opt for GN prep, you never know.
Factory skid plates are usually junk - one good bash and they're usually done for. We've replaced or reinforced all of ours.
Buy your own tires. Maybe make a deal with the dealer to take off the OEs and replace them with ones of your choice prior to delivery.
Finally, you might consider whether or not you'll ever want a flatbed, now, before you buy a truck with a bed (over C&C) or waste the money on a factory bedliner.