It could be regional, but I would guess the auto's sold out first. I remember when I started looking, the dealers seemed to have a lot more auto's than manuals. ( I wanted and got a manual) I also have the nav, not by choice but it was on the car when I bought it. Had everything else I wanted at the time, plus the nav. (and if memory serves me, there was an item or two that came only with the nav package that I wanted). Long term desirability of having nav, who knows. Some will want it, for the ease it provides, (have to admit right now it is nice) but I also have my question of, "what the heck do you do with it when it gets out of date and is obsolete?"
IN the end, get what you want, let the resale and desirable options question work itself out once you do go to sell it. Why drive something that isn't quite what you want just so that it might be more desirable at resale time?
2013 GT 6 spd, GT500 mufflers, BOSS quad exhaust, Roush CAI, Barton shifter & 2 post bracket
CS GT-40 Wheels, Hotchkis sway bars, upper and lower control arms, springs (1.1/1.6 drop) and adj panhard bar KONI yellow struts and shocks J&M caster/camber plates,
BMR Upper control arm mount and lower control arm brackets.