yes, Indirik - that's always been your answer to everything.
Rebel!
Doesn't work (outside of a few basket cases on Dwilight). You are usually the only voice, get to listen to a lot of "do it for the realm" crap, get to deal with fines, bans, threats, etc., get to try to rally silent, apathetic lords to your side
"Leave the Realm - and take your region with you!" - yes, if you are lucky enough to be in a border region, you can. And have them contact your new ruler, asking him to tell you to give the region back because it is "theirs", or to ban you if you don't. Which he often will.
Or you can penalize yourself by throwing away the closest thing to a Duchy you'll probably ever have in the game - a rural region with food to spare.
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The problem is, there are supposed to be checks and balances throughout the game. But most of them only work if the players stand up together as a group. If you have a realm where 90% of the players don't give a !@#$, then you have no checks and balance. You have one vocal knight against the Council and 90% of the realm who just wants you to shut the !@#$ up with your letters of protest so they don't have so much to read and can click their buttons in silence.
Your suggestions are based too much on the "theory of BM", but ignore the practical side.
You pigeonhole every player into two categories, the lame players and you, basically.
There are many realms who are committed to decentralization. And in most cases, it's easy to say that the duke is being greedy for not accepting to pay for the food, because he and his knights usually earn more than the rural lord and his knights do. Furthermore, it's better "for the realm" that caravans be used, since ox carts can result in massive spoilage. And since caravans cost gold to send, it's *normal* that at least a little gold be given for the transfer, so that at least the lord isn't paying for the duke's gold. Arguing for control over one's food supplies is not that difficult.
And I really have a hard time accepting that there are so many of these unbreakable governmental molds where lower-placed nobles can't decide much on their own if there is an option to delegate the power. In Enweil, way back when I hadn't really earned a place for myself, I ended up becoming a marshal, and was frustrated by the incompetance of the general. The general kept getting re-elected because he was a long-time realm member and respected by many influential people who saw me as being probably more of a threat than anything, despite him being bad at it. And at the time, nothing was really moving in Enweil, it was quite stagnant. And yet, my little marshal eventually got fed up with the general and decided to completely and blatantly ignore his orders, stating that his army would no longer be following the general's commands. By your arguments, the institution that is the established realm should have come to crush this new noble thinking he could do things on his own instead of letting the general, a long-timer, decide everything. But they didn't. And I wasn't marshal of some random bureaucratic army, I was marshal of the main army.
Don't assume that every time a person in power is granted the opportunity to centralize power onto himself, he would do so. Some would, but many wouldn't. And that some realms do it while others don't would be a good thing, it would create another aspect for which governance would vary from realm to realm. And the more possibilities there are, the less identical governments there will be, and therefore the less ideological "natural allies" there will be.