I was sufficiently intrigued by your post that I decided to finally join after some months of lurking. So hi.
What I do think you're doing is explaining exactly how modern basketball is coached, however. You are though, IMO, missing a couple of points and I'm curious as to how you'd deal with them.
1) Take Ray Allen (yeah, booo etc.) You would assume that under that system he would -only- take 3s. You could argue, however, that the only reason he doesn't do so already is because he's both playing against a defender AND a shot clock. You can't expect the defender to stand still no more than you can keep passing indefinitely until he has the exact shot you want him to take. Hence he is going to have to take inferior shots eventually.
2) Keep with the previous example, but let's say the shot clock and the opponent aren't factors. You can say that Ray Allen's best shot is the 3 based on FG% but that doesn't really tell you the whole story. His exact best shot could be the Left Corner 3 but his 2nd best shot could be the the Top-Right Long 2 (not saying it is, just an example). FG% doesn't tell you that. Coaches, however, do seem to take that into account when drawing up plays, though.
3) The whole system is based on player analysis upfront. You're assuming you already know what shots the player is best at when he joins the team. But, realistically, you can't know that about all the players. What happens when you draft a kid, or you trade for a young player who hasn't played much? How are you going to find out their best shot if you keep forcing them to shoot their best shot from within a previous limited sample? How could he develop alternatives?
Very interesting post, in all.