Zero reason the 9th best team deserves the #1 overall pick. That system would end up permanently burring teams like the Pirates, Orioles, etc.
Baseball needs to adopt similar methods that we see with other leagues. The lottery would be interesting for the top 5 or so picks. Also, allow picks to be traded. This one alone would prevent the need to tank a roster for years. The draft's purpose is to give bad/terrible teams a sense of hope for the future, not reward mediocrity or a "just not quite good enough" effort.