well its not only master quest, all end game content need to be extremely hard, dragons need to be demigods, etc etc
master quest is another thing, right now is nearly a joke but its not so hard to fix this
your suggestions are all good, but most of them should also go on other monsters
the final boss though should have all of that stuff and more
Generally you may be correct, but I prefer not to have auto-scaling for this reason: if something is easy, you get a crappy reward (an item you won't use, 35 gildar that doesn't mean anything to you at this point in the game, etc. This also gives a good way to level-up later champions (and henchment). I would say that for the master quest, auto-scaling is allowable because the reward--winning the game--has a value of infinity (so to speak) so it must always be a difficult fight. I do agree that the top-end things should be harder, but perhaps this has to do with what MiamiBigAL said about heroes being super-powerful.
I think the main problem is with champion-scaling. It is relatively easy to get high level unstoppable champions. I think that regardless of scaling the last boss should be a lot tougher anyway. Maybe make him magic immune like the obsidian golems. Slow/Haste alone makes him a piece of piss to beat.
I think you are right about the champions, and maybe that has been/will be fixed. A good test would be for me to go back with all my top-level troops and see how it goes.
As for magic-immune, I think maybe 90% resistance would be good. In Baldur's Gate II, you could eventually wear a dragon down by casting reduce-magic-resist spells and then plinking away until something got through. It felt, to me, pretty epic to have your fighters trying to hold on while your mages tried to get something through. So I stand by my earlier if-you-get-slow-after-5-tries-it's-ok statement. But maybe 5 tries should be more like 10 (or just salt and pepper to taste).
I also think it would be cool if you could have a "Wait, just one more turn..." option when you win where your sovereign has a summon-badass-dragon spell and you could conquer the rest of the world for fun. But there are certainly higher priority things to be done.