So many thoughts...
Quick answer is "Yes they should be integrated" (actually there's an argument that they are supposed to be if you are to go by FIFA's regulations). Will they ever? I doubt it, it shakes too much the established power structure here. The argument that Academies are there for money (and therefore should be shunned for the BCSA sanctioned path) is laughable. As far as I know, any pro team in the world is there to win tittles and $$ and their academies are one of the ways to accomplish that. I don't think Spaniards, Germans, Brazilians, etc. are complaining about the money side getting into the picture. I have in the past questioned the structure here, preached that academies be included in the system, etc., while at the same time getting my "badges" and coaching club soccer. Eventually just got tired and focused on watching my kids play.
Anyhow, I digress... All I can say about the relative merits of FPs and NFPs is talk from experience. Both my boys played in NFP club teams growing up and were good (as well as obsessed) enough to always play at the highest level available here, be it Select than Metro and BCSPL. But I also had them in academies (since, I dunno, 7?) and so they went thru WC's, Roman Tulis, TSS as well as Metro Ford's and SU's. To the point that I was never shy to say that if I had to choose between them going to their FP Academy or playing club soccer (at the beginning some BCSPL clubs were trying to make players choose their path with exclusivity) Youth soccer would be a goner. Why? Simple, I'm Brazilian and there's really no other sport, right?Did it pay-off financially or development-wise? Frankly, I never cared, but if you buy into the 10,000 hours argument, they were definitely exposed to lots more football than they would otherwise be and their "soccer resume" certainly reflects that.
My advice for parents who consider academies has always been: go for it but be realistic in your expectations. Don't expect your kid to become the next Messi, he most probably won't. Don't expect for the investment in BSCPL and Academies to pay off in savings on their college education. Just put the money aside, you'll probably be better off. BTW, no sour grapes here, both my kids plaid Varsity in college and one is in a NCAA D1 full-ride. But I know it's just luck that the investment paid off for him. If he had chosen to play for, say UBC, all that money would be down the drain...Anyways, do it because your kid love the sport and can't have enough of it. Do it because the kid wants in the late Roman Tulis' moto "Be The Best That He Can Be" whatever that level is.
I agree - if you are putting your kid in any league expecting/hoping to get money back for your "investment" (university funds or pro soccer contract) take a step back because it won't happen. No one here will become Messi. Give that dream up immediately.