Honestly I've thought these things a few times since I for possibly the last two football manager versions have failed to attract/produce a youth player beyond 3 stars at any club I've managed. Best facilities at most of the clubs I've managed at some point (initially or built up to), top staff throughout senior and youth setup - with a top head of youth development in this version and top scouts, and top reputation with even being the number 1 club in the world.
My opinion: its just luck. Pure luck. Sure I've seen some people's games produce astoundingly good players from real minnows though I'm sure some of those people were telling porky pies, I believe that at least some of them were fortunate to get a world class player come through their ranks. It's accurate afterall that not only the big clubs turn up the gems of the future, more often than not you see Manchester United buying youth prospects from all the country and world to stick into their youth academy, so the model of having to buy in isn't exactly wrong, just annoying.
I'm currently playing with Sao Paulo in Brazil, one of the biggest clubs out there and to my knowledge (at least in my game) they have the best youth setup and ability to pull in talented youngsters in the country, yet in the three seasons I've played so far I have yet to generate a player more than 2 stars....in the top youth system club in Brazil....where young stars are generated like no tomorrow.
So yeah, luck.