The main idea has been to disincentivize bottom of the barrel teams to play worse on purpose, essentially tanking in order to improve their draft position. This has been adopted many many of the major sports leagues as well and has proven to be fair.
In summary, it is only the second year that the MLB is utilizing this new draft program, so it is still up in there on how well it works for the MLB. Last year the Pittsburgh Pirates increased their draft stick from 3rd to 1st and the Detroit Tigers went from position 6 to 3.
No doubt about it, there will be winners and losers when it comes to the lottery, but its keeps the game fair and in a better state. And for us Blue Jays fans, according to a recent simulator, there will be picking first!