IMO, this is an aspect of the game that deserves immediate attention, not because it's fatally flawed, but because it could so easily be improved.
There should be 3 levels of feeders: High School, 2-Year College and 4-Year College. High School should feed 2-Year College, 4-Year College and the major league draft, while 2-Year College should feed 4-Year College and the draft, and 4-Year College should feed only the draft.
Also,
team financials should be available. One should at least be able to set market size, fan interest/loyalty, cash, budget, merchandising and media contracts to help distinguish the elite programs from the less successful programs.
And even though monetary contracts shouldn't be given to players in feeder leagues, there should be a free agency system for the 2-Year College and 4-Year College levels that would allow a simulated form of "recruiting" from the High School level.
I've found that most everything else can be handled within the current setup, although I admit it would be nice if the optimal settings for each level were already set by default.
The bottom line is, the feeder system needs some minor (albeit important) adjustments, but it shouldn't require a complete overhaul. Is it something that could even be corrected in a patch?
Only Markus knows for sure.