Well...when Austin Aries won the belt he created the A Double L Double (Austin Aries Lethal Lottery) to select who got title shots. Jim Cornette returned to say Aries wouldn't be hand picking his opponents anymore and for a wrestler to get a title shot has to be in the pick 6. The concept in theory isn't that bad.
However like you said, the system has way too many flaws. Recently Cluadio lost his #1 spot because he didn't defend his spot, even though he was booked in a tag matches. The ROH fans were pretty upset about this. Then you have ranked 4-6 getting title shots and 1-3 weren't getting shots. Anyone can come in a get the #1 spot over night, even though it's not supposed to be a "ranking"
All in all, i don't mind it too much. It does make the undercard matches mean a little more. I just wish they paid more attention and the guys at the top of the pick 6 were guaranteed title shots.