Hey, first post here.
First of all, let me say that I'm not in the US, but I guess things dont change that much from country to country. Or maybe they do.
What doesn't change is that in the military, any student who doesn't achieve certain level is dropped from dropped from training and sent to perform any other non-flying duty. Is this important? I think so.
As a civilian, I might fail my exam 20 times before getting my licence. In the military, I cant't do that.
Apart from this, all military pilots get full IFR/IMC training. Not all civilian (GA pilots) get this level of education.
All military pilots travel, get to know different climates, different landscapes. In my country, the deploy south, they get to fly in windy and freezing conditions. They deploy north and they get to know how is it to take-off from elevated airports or in desert-like areas, then move west to get some mountain flying and east to get some flight hours over the ocean (well, all this is theoretical since they dont get much flying hours, but anyway, you get the point). Not all civilian pilots do this.
Taking all this into account, it is easy to confirm that military pilots are, in most cases, better trained.
But when it comes to decide which is the "best pilot", lets first define "best pilot".
IMO, this cant be established. An airline pilot might require to have good communication and instrumental skills, while a stunt pilot might require good stick'n rudder skills, etc.
I've seen former A-4 Skyhawk pilot (who also flew transport aircrafts) who couldnt make into the Captain seat (he basically failed the course) in ARSA. So, assuming that ex-military guys are always better prepared is nonsense.
Other A-4 pilot got out of the Air Force and went to fly...firefighting airplanes. Yeah, he couldn't get a job in an airline in a country for very few pilots.
Transport/Taker pilots might be better suited than fighter pilots for the airline industry, since they have experience in -almost- the same type of aircraft. But again, there's no guarantee in this.
For the airline industry, flying safer is better that flying aggressively showing off skills. Knowing how to properly do a SID/STAR is much more important than being able to sustain 9G's. Landing smoothly is way better than knowing how to perform a short take-off in a C-130.
What I mean is that, even when, doubtlessly, military guys may learn a ton of skills that are not present in the civilian world, those skills might not be necessary to be an efficient and safe (a GREAT) airline or GA pilot.