The fact that legislation is always vague and they can interpret it to mean whatever their ideology wants it to mean is just waiting for more legislation to fix it. If there is an obvious miscarriage of justice, all you need to do is get a majority of the House, 60% of the Senate, and the President to all agree within a two year window. There, justice done.
In this case the guy got to go all the way to the top court. That's great. That sounds like a good system so far. So at very least it's not rotten to the core. Thomas is unfit and disappointingly partisan, but this appointment came from the executive branch, not the justice system itself. The justice system was set up so the executive branch can check the judiciary. In this case the executive Branch's actions really messed up, but I don't think it's fair to criticize the justice system.