My thought is this...random allows for there to be AAA "winners and losers" as luck of the draw is just that. Some owners get quality players and others get duds. Allowing trading of AAA can help if you get duds, but also opens the "trade rape" issue.
With manual drafting, you essentially pick your poison. You have control over quality/quantity, defense and every other factor. This allows for more fine tuning but also for more gamesmanship of PAs/IP.