It's very easily fixed if they want it to be.
They need to publish written reasonings for their decisions either way.
That alone would clear up 90% of the bad calls, because as soon as they're made to explain the utterly inexplicable decisions, they'll be scrutinised, the public and media will go mad if they come out with bullshit, there will be a record of their incompetence and they will know can't get away with them.
The other thing is they just need to get used to overruling each other and accept it's not a big deal like every other sport in the world has managed to.
Binning Mike Riley will be the cherry on top.
As it is, I suspect we will get more right decisions but the time delay will go up next season when they use the monitors.