Work with better shops.
Plenty of shops do great work, and plenty of amateurs do terrible work. It goes both ways.
To make money as a shop doing gears, it takes one thing: NO COMEBACKS.
Work with better shops! This does not mean 4wp!
X2.
I know in the automotive repair industry, it's sometimes harder to find good mechanics. I usually do the majority of the work on all my cars and have ever since I started driving. But I do draw the line at gear set up. I always pull the axles, take them apart, clean them up, and drop them off at a reputable shop. I always use one that specializes in axles only. (Pro Gear in San Diego)
It's not that I couldn't set up the axles, but the tools and the learning curve are more than I want to take on. Coupled with the fact that you won't know if you effed up until the axle is all assembled, installed, and ran for a while. I don't care to take that chance with my expensive parts a la Evan. But each to his own.
Part of the problem is that the majority of Jeep owners tend to be notoriously cheap, at least in my experience, and just naturally seek out the cheapest option. Sometimes it's better to pay a little bit more and get good results. Many people are locked into this notion of false economy.
As far as professionals vs amateurs, I don't agree with Anaks assessment. (I do respect Anak and his contributions to this site, however. Not a bashing whatsoever.) I think it depends greatly on the industry and the task you're trying to accomplish. Sure if you're talking about gardening/landscaping, but I don't want an amateur performing brain surgery on me. In my line of work, remodeling, I fix work butchered by the amateur homeowner countless amounts of time.
It depends on the person, their skill set, the task they are trying to do, and a number of other variables. But to say the amateur is better than the professional is not a blanket statement, IMO.
Like XCM said, find a better shop.