There are plenty of reasons to not like the Allocation system. It is inherently an anti-capitalistic way of talent dispersal and forced parity. What is often ignored, are some of the advantages of the system. Take today's Benny Feilhaber saga where one of 18 teams has a shot at getting the dynamic attacking midfielder. All of MLS cares, because it is not a contest between 3 or 4 big money sides (Los Angeles Galaxy, New York Red Bulls, Seattle Sounders and Toronto FC). Instead teams like Chivas USA, Houston Dynamo, New England Revolution, Sporting KC and Phildelphia Union are connected to acquiring Feilhaber. Having 8 teams connected is better for the League than having 4 connected.
The allocation system gets more intriguing when one thinks that who ever gets Benny now gets stricken from the list of possible returning USMNT players like Eddie Johnson, Damarcus Beasley and Freddy Adu. These connections are no longer just dreams of my own, but in "serious press."
If you are interested in the decision process of general managers, observing the allocation process allows a more direct view of how certain players and needs are balanced. Does a team take a Feihaber now and pass up a Marcus Hahnemann later? How much talent should be traded away to acquire one of these players? Does marketing count as much as improved play on the field?
In a free agency world the process is simple - we have more money and will sign him. Process over. It is rather dull and boring.
As an aside - his contract is not a DP level (Goff estimates 300k$). If Seattle were to trade for him (to move up in allocation order as currently 8th) they would likely open up cap space in the deal. It is unlikely though that they could acquire two USMNT within a single year (though one could argue DC United did with Troy Perkins and Charlie Davies).