My truck has a NV4500. NV4500s are known for fifth gear issues and must use a costly oil due to synchronizer material. That truck you looked at; I'm guessing it's a NV3500, so do some research on known issues.
I'm not hard on clutches despite regularly pulling, but I've had two replaced due to collateral damage from either leaking ***** cylinder or throwout bearings. That's over~250K mileage, though, so that's not bad. I lost fifth gear about midway in the mileage. The truck I had before that (2G 1500) had a Getrag (I think), and saw the same duty but never had issues..go figure.
I don't know you'd have better fuel economy, given AT have lock-up torque converters and overdrive. My 3G 2500 4X4 Hemi gets ~12.5 MPG unladen on the highway. Judging from the thread about MPG, that seems consistent with others. I'm pretty sure the same setup with an AT would do that well.
Getting stuck with a MT means you might ride the clutch trying to free yourself, and if you're rocking to get momentum, an AT responds quicker.
Living in an area with lots of traffic and lights isn't fun with a MT.
Last thing to consider is the cost of rebuilding. I don't know you'd come out better on rebuilding a MT, and it seems there's less places doing it.
Pros: I think you might have less chance of people wanting to borrow your truck or steal it with an MT.
Driving is more engaging with a MT, given the need for shifting. Personally, I like being attenuated to my truck rather than in a sensory deprivation tank.