I think it would be nice to reward guys who perform well so guys get paid market value w/o hurting the team substantially. George John comes to mind. That guy earns like 50k a year. He has his mind set on leaving asap b/c the wages here are ridiculous. Dallas doesn't benefit from giving him a raise while he's on his rookie contract so the only way for him to earn a decent salary would be to leave. Ream is another example that could've become a John had he not been sold.
I agree with you, and it would be nice. Just don't see it happening for awhile. From what I know both Ream and John rejected any and all extensions so they could leave when they want. Problem with MLS is they'll usually only offer 4 yr deals, like the one Shea signed and make it tough to leave when you want and European clubs start bidding. If MLS would offer a 21/22 yr old such as Shea a 2 year/500K per year deal(similar to the 2 year deal Bradley signed with Chievo, which leaves him with options), that would be great. But they generally will offer 4 years, at about 200-250K per year so you can't leave until 25 or 26, and make it tough in general to leave in your mid 20's. Every young player needs options in their early to mid 20's.
Guys like Ream who left, and John or Cameron have to leave to make the next step at they're all entering their mid 20's. If they sign extensions it becomes much tougher.