You can do an aftermarket one as you stated, and can get a lot more options out of the unit vs the factory one. For instance in my '04 I had the units pulsed negative outputs control my headlights, my reverse/upper cab lights and had another output to turn the heated mirrors on after the truck started. This of course was a lot of work and I needed to build an external latching circuit to make most of the funcitons work..
Also, you would obviously have to have the aftermarket key fob along with the factory integrated key fob because that's your key now, where as before you could just dump the factory remote. Not a big deal but just more to have in your pocket. For any installers out there it isn't a terribly hard install but you will need the DBALL unit to integrate the aftermarket brain into "tricking" the truck to start. You however will not have to sacrifice a key like the old transponder units.
If your just looking for an Auto start and nothing else, I would do the factory unit yourself and then take it to the dealer to be flashed. I haven't done one yet myself, but the instructions look super simple..