Your last point is a little more difficult but I still think I would let the handicap system work. I don't see a situation where a competent captain would put up in such a way that a higher ranked player would always lose.
I could probably support handicap adjustments if there were a handicap committee comprised of higher ranked players who could be trusted to make objective decisions. Unfortunately, I saw bizarre situations when I played APA.
One individual who had played for over ten years gets lowered from a 4 to a 3 in the Regionals and wins a trip to Vegas. After Vegas, he gets raised back to a 4. Everyone in the league knew he was actually a 5 but if you complained, someone on your team would be raised.
Another individual who was a known player and an obvious 7 in 8 Ball started as a 3. Stayed a 3 for several weeks, then moved to a 5, then got lowered back to a 4. Everyone, except apparently the LO, knew this guy was a world beater.
So one guy was lowered in spite of their stats and another should have been at maximum skill level and wasn't. If the LO is going to override the handicap system, they should have good players they trust advising them.
We'll have to agree to disagree on Johnny. If I know a number isn't right, I make it right if I can. Accuracy of the numbers is my number one job. That said, if I think the player will get there on their own, I let it happen naturally.
Here's the catch, and it's related to your examples. The LO can only lower a skill level if the player is already calculating at the lower level and is being artificially held up by an override. Even then, the LO can't do it (any more, they used to be able to) if it violates the lowest attainable rule. Only the national office can force a skill level down when the calculation or lowest attainable rule says otherwise, and that would only be under special circumstances, usually medical.
So, if you're calculating at 4 I can't make you a 3. I can make you a 5, but not a 3.
I take the conspiracy theory stories with a grain of salt. Knowing how the system works, and what the LO can/cannot do, gives me an edge in determining how much might be true and how much is speculation. Take your first bizarre scenario, for example. The LO can't let someone drop in regionals (or any other time) unless that player is calculating at the lower level and has never been higher than the level from which they are dropping. Soooo, in this bizarre scenario I can assure you that the LO didn't do anything that you haven't said in this thread that you would favor. In fact, the LO probably didn't do anything at all. If I remove the conspiracy theory part of your scenario, I get "A player came into regionals as a 4 and dropped to a 3. After winning some matches and getting to Nationals, the player went back up to a 4." Why do you find this scenario bizarre? As for the part about raising someone on your team if you question the movement, that's probably more conspiracy theory fueled by a coincidence or two.
I especially like your second scenario. That's Johnny. You're in favor of letting hypothetical Johnny play at the calculated number, but you consider the real-life Johnny a bizarre situation? Remember, the LO can't make him a 4 if he's calculating at 7, so he had to be calculating at 4. Are you trying to say he was cheating and the LO knew it and did nothing?
Most of us do have good players we trust advising us. I do. Many of us are pretty good players ourselves, but as justadub said, we can't be everywhere. So we recruit people to help, good players who are going to be there anyway. Often we don't tell anyone who they are or that they even exist, because we don't want them taking the heat when skill levels change. And believe me, there's a lot of heat. I'll take all the heat, that's my job, and as long as I'm focused on getting the numbers right people can say what they want.