OK, so I'll just throw this one out there. I completely believe that Disney is not going to change a thing, and continue with the boarding passes. But here, for purposes of this board, is my suggestion.
Go ahead with the Boarding Passes. But limit them somewhat more than they currently are. Then also allow a Stand By line. Make it known that if you are in that line, there are no guarantees as to how long it may take before you get on the ride. Could be 3 hours, could be 8 hours. Then pick a time, say 2:00 PM, and say that each day, the Stand By line will be cut off, meaning no more people can enter it. So while it will be more difficult to get into a "guaranteed" boarding group, for those who MUST get on the ride that day, the Stand By line will be an option. You may spend half of your Disneyland day in that line, but for all intents & purposes, you will get on eventually.
That will make the Backup groups the least desirable place to be, since those will only get called if it's a good day for the ride, i.e. few breakdowns. My solution allows people an option. If people complained, Disney could say, "well the demand is just so enormous, there is no way we can accommodate every single visitor. But if you are willing to wait, the Stand By line will afford you the opportunity of riding at some point today.
Of course, it's not perfect, it's not ideal, but no process would be. But the way it is now, I think Disney is disingenuous by advertising a ride that it is both a time consuming process, with absolutely no assurance of success. And if you're unsuccessful in those 90 seconds, you're shut out for the next 16 hours, and nothing you can do about it.