A draft system itself is a great idea, you worked out the advantages, but they won´t apply on a 3vs3 with to changes. You can totally rebuild your team so building up a counter team is impossible. in a 5vs5 with two changes you have to reveal at least the direction your team heading to.
What i would love to see is an alternate picking of heroes somehow like this:
Player1 picks first, then Player2. Player1, Player2, Player1, Player2 double picks, Player1 double pics and at last Player2 picks his last Hero.
5 seconds to choose your hero, 7 for the double pick.
A better sorting of heroes in the pick screen would be needed though.