Like you've mentioned above, the Zach Pfeffer thing REALLY got me interested. As a youth soccer coach for the past 7 years, the youth side of the game always catches my interest. How/why clubs do things different from other clubs etc etc. Anyway, when I say this deal, going to a 2nd division German club, I found it incredibly strange. It was only when I looked into it further, like you say, that he'd hardly have any games here.
I think the MLS needs another expansion team to round up the number and to lower the number of play off teams(IMHO there should only be 4 in the play offs, its FAR too large) and then they really need to concentrate on the structure/youths. Every league should mirror the rest, and they should work in partnership with each other. With proper reserve/youth leagues for the MLS teams also. They could have their reserve teams within this structure also like they do in the Spanish leagues but I think this is what the USL Pro thing is (I've not had the chance to properly look at how it's gonna work)
I agree with the salary cap thing regarding the homegrown players. What is it now? I'm not too sure? I'd probably go with the suggestion that they don't count if they're U23 or something similar. This would mean that the club could bring them through and if they're a proper talent at 22 but don't fit into their salary cap/structure, they could trade/sell/release the player but they've at least got some proper development behind them.
Btw, I would never consider myself as a 'soccer insider'!!! I'm just lucky enough to be involved in the game on a daily basis as my job, and I consider myself very lucky to be on the field coaching players that will hopefully follow their dreams to making it pro.