Sounds like you're making an argument to decrease the amount of control an organization has over a young player instead of scrapping the draft. I concur with decreasing 6+ years of control on a young player.
...or to allow for freedom for a player to choose where he plays his career.
If I'm Sean Hjelle two years ago, for instance, I'd want badly to be part of the Tampa Bay Rays. They've been renowned in the industry for their work with tall pitchers. However, he's forced into a system where he's selected by a team and then forced to negotiate his bonus only with that one team.
A top-30 player like Maurice Hampton would likely not be headed to college if he had the ability to negotiate with all teams from the get-go rather than being forced into draft slots and bonus pools of the team that drafted him, meaning as soon as he got past the first 45 picks or so, he was beyond where his signing bonus demands made sense.
Having not seen Mike's piece yet (but I will!), one thought I'd throw out would be to have a bonus pool based on record, and a team like the White Sox could have chosen to spend $7.2M of their $11.565M (assuming bonus pools were the same) on Andrew Vaughn, or they could have chosen instead to spend the same $7.2M to outspend the teams that signed Kody Hoese, Logan Wyatt, Jacob Sanford, and Tommy Henry with money left over to meet the reported bonus demands of top-50 prospect Spencer Jones. They may have chosen to go with Vaughn still, but it would be certainly worthwhile to have the choice for teams and players both.