I agree with you that the entire system is slanted in some players/parents/clubs/leagues favor. It's unfortunate that a game that seems so simple is also so easily exploited.on the boys side, the academies wouldn't have the cannon fodder they need given the distances in the US.
The other main function against them is to act as a way to sort talent without having to do the distortions of a pro/rel system, which is where we get into the accusation implied by the OP: that it's really just a way to lower competition between the clubs since having an ECNL or MLS slot is a golden ticket to attracting talent not just to the first but also the lower teams.
The old coast pro/rel system just didn't work which is why it fell apart: too much variance in field and staff quality, too many teams locked out of any real chance of improvement, too many short cuts taken to advance up that pyramid.
I, however, don't really see a way to fix it short of establishing a national governance system that can regulate things. However, that means blowing up even AYSO and that's simply not going to happen.
The one "game changer" that I've seen in youth soccer is the rankings app. I still don't like it for individual game predictions. But it's very good at giving a true high level view of the teams/clubs/leagues that are performing. Before the rankings app everything came down to my XYZ is better than yours.
In the future there's going to be RFID tags sewn into jerseys and implanted in thr ball. The scores will be tracked in real time. This might sound scary to some but it's going to open many doors for those that were previously overlooked becuase of politics and/or who you know. It's already happened to some degree with the different leagues.