My parents are looking at getting a FJC to replace their old '91 Explorer. Anything that existing owners would recommend asking the dealer about, options to avoid or get etc. It will most likely be a base model since the most off-roading it will see will be logging roads or forest service roads. Having lockers would probably increase the resale value however they plan to keep it for the long term so resale isn't a concern.
For sure get some fisheye mirrors to stick on the side mirrors. This will eliminate the FJ's considerable blind spot. Don't waste your money on the factory skid plate. It is weak as a tin can. They might want to wait until the new reinforced fender aprons go into production so you won't have to worry about the fender bulge issue. Other than that get ready to have the sweetest rig you've ever driven. I didn't think it was possible to love an inanimate object so much.