My friend Jimmy Golen, writing for the Associated Press, tackles that puzzling question.
As another friend, the economist Richard Thaler, says in the piece:
I cannot think of any good reason why MLB would have such a rule, unless it is worried that the teams with the highest picks are not capable of making good decisions…it has to help the teams with the top picks to have the option of trading them for additional picks.

I’m surprised they didn’t mention how much it keeps down the price of players, which is why baseball does a lot of things (luxury tax, revenue sharing, etc.). I’d bet that the Yankees or Red Sox would have paid a lot more for Strasburg than the 15M or so the Nationals did, especially if they’d had to pay out big time to get the pick. (Consider how much the Sox paid for Matsusaka once they’d paid 50M for the right to negotiate with him.)
The issue might be that while teams have infinite lives, the general managers don’t. So while it might not be in the team’s best interest to trade away its picks for the next 10 years, a general manager might try it since if it doesn’t work, he’ll be fired anyway.
I think the NFL and NBA have similar rules about not trading away 1st round picks in consecutive years.
I think John T and Fred have it right. Look at what Eli Manning did to San Diego, forcing them to trade him to the New Jersey Giants. If you know the teams at the beginning of the draft are all small market teams this year and they likely will be again next year and there is no way of escaping from the draft, you have to submit.
Back in 1996, with the help of Scott Boras, four players found a loop hole to escape the draft. Matt White was one. I don’t recall the others. White signed for over $10m, an amount few draft picks have ever received, and never had meaningful MLB playing time. The four signed for a total of $30m. Thirteen years later, the top 4 picks (including once in a generation prospect Strasburg) in 2009 signed for a record $30m ($15m/$7.5m/$6m/$2.5m) with Boras representing the top 3 picks. Constraining mobility lowers labor prices.
#8′s rationale makes by far the most sense. The league would much rather conspire against rookies than against its own small market teams.
The free agent compensation system has changed over the years. At one time, teams actually could get a player back in compensation. Weirdly enough, that player was not necessarily from the team that signed the free agent!
Teams still *do* get compensatory picks, unlike as stated in #4, but only if the original team offered the free agent arbitration.
The slotting system is voluntary. The Commissioner’s office recommends the slots, but there is nothing to prevent a team from going over slot, and teams often do.
Any kind of cap on draftee pay would probably have to be negotiated with the MLBPA, and I doubt that the MLBPA will allow it without some pretty tasty concessions.
I staunchly oppose any kind of salary cap, and I would support allowing teams to trade draft picks. If two teams are able to reach a mutually agreeable deal involving draft picks, I see no rational reason for the rule preventing that from happening.
It’s widely believed right now that a hard-slotting system will be put in place next CBA (2012). This actually favors small-market teams, as no longer can the Yankees and Red Sox pay players over-slot bonuses and have those players scare off teams less likely to do so.
The time Moneyball was written is very different from baseball in 2010, as nearly every front-office values sabermetrics and the draft highly, as well as understands the value of the current free-agency rules and cost-controlled players.
MLB’s thoughts on the issue
http://mlb.mlb.com/news/article.jsp?ymd=20091215&content_id=7811316&vkey=news_mlb&fext=.jsp&c_id=mlb
The rich teams basically already use the draft as free agency. They draft high schoolers who are set to go to college in the 15th round, and lure them away with overslotted signing bonuses, poorer teams with high draft choices stay away from top talent due to “signability” issues, and many of the best players are taken from the international market, that requires no draft choices, and heavily favors the rich teams.
Not allowing the trading of draft picks is the one thing that the MLB does to help the worse off teams. Otherwise, the Yankees would essentially just buy the #1 overall pick every year. The league needs a draft slot cap, salary cap, and salary floor.