Having all of the leagues under one umbrella and have a system of promotion/relegation should be the goal. Youth leagues with promotion/relegation, Adult leagues with promotion/relegation. No $100 million dollar fee to get in the MLS. New England, DC United, Colorado and Minnesota relegated. Charleston, Louisiville, San Antonio and Real Monarchs promoted. Etc... if you beleive that the MLS is the highest level and the USL a step down.
Unfortunately, there is too much money being made by old men with deep pockets to allow this to happen. Why does the US soccer federation have a $100 million dollar war chest? Because this is a for profit business, not the non-profit organization it is supposed to be.
They have the money right now, $100 Million!!!! to consolidate all these leagues, make it one big national program. Spend it on the players you have built your wealth on, build it for the future. No they will continue to hoard the money and use it to enrich the owners at the top, protect themselves.
Heck I am part of the problem. My DD plays for and "LA Galaxy" franchise. Her uniform says LA Galaxy, her bag says LA Galaxy, half of her wardrobe says LA Galaxy, yet her local club operates under the guise of a non-profit 501 c3. Every time she puts on that uniform and represents her club she is promoting the brand. Building profits for the fat cats at the top.