Drawbacks to Factory Nav:
1: Expense
2: Can't use while driving (must program while vehicle is stopped) (unless you employ one of the mods you can find on this site, either software or wiring changes)
3: Updates for maps are expensive
4: Some aftermarket systems have added functionality
But. . .
Factory is nicely integrated to the stereo, phone, truck.
It is very functional, e.g. it knows where all the gas stations are, phone numbers for restaurants and hotels, and will dial them for you directly if you have bluetooth and right phone.
I chose factory nav., as I didn't want to end up fiddling around too much with my truck. I wanted the stereo (I don't need some zillion dollar system, my ears aren't that good).
And I wanted full bluetooth integration (anticipating cell-phone use laws here soon).
I guess if I had a truck without it, I'd look at
ebay.
Good luck