I'm debating where to send my kid, too, but she's young enough and has only been playing for a year, so that I don't think we've maxed out the potential at the junior program where where we went last year. The problem was that the instructor is a guy who loves golf, likes and gets along great with everyone (knew dozens of course regulars by name), likes kids, but did not show much interest at all in really teaching the kids in the program. In the first few lessions, there were only two kids and he mentioned in an aside to me that the other kid had already had one or two previous sessions' worth of experience, and was hopeless. Yes, her up-and-down stroke was as close to what one sees watching someone use a pickaxe to dig a hole as it resembled a golf swing. All aspects of her game clearly required a lot of help, but he mostly left her to whacking balls 10 feet downrange. The pro had given up on that kid and spent about 80% of his time instructing my daughter, when he wasn't smacking a few stylish pitches at the target flags with his wedge. It benefitted my daughter, who does have some natural skills, but was not fair to the other kid and I could not help wondering what would happen with my daughter when the next Michelle Wie or Lexi Thompson came along in the course and he switched his attention to her instead. Even though my daughter was one of his favorites when more kids enrolled in the second session, week after week she still had the same too-upright swing plane. As kids often do, she stubbornly refused to take advice from dad and I had to ask the pro to work on that issue with her, something that a high handicapper with a sometimes vague knowledge of the golf swing like myself should not have had to do.
From my experience at least, it seems that a fair number of instructors and coaches out there who teach in junior sports programs don't actually enjoy teaching kids and do a half-assed job of it, at least at the beginning levels. We had the same problem when I enrolled my daughter last year in tennis lessons at the local country club. Both of the two assistant pros in charge of the youngest lessons seemed pretty bored with it and just ran the kids through a lot of the same drills week after week without actually doing any instruction on grip, strokes, footwork, etc... instead showing off their volleying skills trying to keep the kids' shots in play. A five or six year old in his/her first weeks of lessons isn't going to appreciate the difference between a Western and a Continental grip, but they needed to be doing something more than just lobbing the large foam training balls to the kids. I had to go up to the two pros before a lession and tell them that I noticed my daughter was missing most of her shots because she was standing too close to the ball and it was coming inside of her swing every time and ask them to work on that with her. An NTRP 3.5 rated player shouldn't be telling a tennis pro how to do his job and I didn't want to seem like the Overbearing Sports Dad, but was I supposed to just do nothing as my daughter was swinging-and-missing time after time? This year we enrolled her in the next level of lessons and I was really pleased to see that within the first five minutes, a different assistant pro called her up to the net, adjusted her grip, and gave her 30 seconds of actual instruction, resulting in a lot more shots going in and a big smile on my daughter's face - that's the kind of instruction I want my kid to receive in any sport.
Unfortunately, at another local course where I was thinking of enrolling her in golf lessons this spring, we had an issue with an instructor who seemed to like kids too much that knocked that program out of consideration. We stopped by their booth at the annual pre-season golf expo and one of the assistants who does their junior program (she looked a bit like Laura Davies) was inappropriately friendly with my daughter, putting her arm around her and petting her head,which weirded both of us out and we left quickly. Weeks later, when talking about golf for the upcoming season, my daughter suddenly said "Daddy, please don't make me have lessons with that creepy lady who kept touching me." When I realized how disturbing that encounter had been for my daughter (even though it probably - I hope - was simply innocent friendliness), I wrote to the head pro, described the incident, and suggested a reminder to the assistants that it is not appropriate to touch kids (outside of purely instructional adjustment of hands, arms, shoulders, etc...). In the post-Jerry Sandusky world, I don't understand how anyone would think that anying more than a high-five is appropriate with a kid.
Rob, I'd say that if you have seen the same swing flaws over the course of two seasons, your son's instructor is not doing a good job and you should find someone else. At a bare minimum, approach the instructor after a lesson, say "I've noticed that my kid has XYZ swing flaw - I'm wondering why you haven't addressed that in your lessons" and see what he/she says. Maybe call up some local high school and college golf team coaches and ask them for a recommendation?