Looks like you don't fully understand why militias are big problems in general.
I am not talking about just peasant militias. Despite them having their own set of issues, normal militias people are putting to defend are causing too many issues.
1) Militias are as strong as player controlled units
--Their only disadvantage is the fact they can't move. Why should they, units without any commander, be as strong as player controlled units?
2) Even when you can't pay them, they don't desert like player controlled units. A small portion of them will leave but not significant enough to deter even small regions without any capability of paying militias to recruit a lot of them.
--If a region can't pay for militias, they should burn the region to the ground and take all the gold and leave. Mind you, these militias are paid soldiers. In BM you are not commanding retinues or soldiers from your holdings. You are literally buying mercenaries off the market. That is why they will beat you up and take all your gold when you fail to pay them. You are bound by a contract to pay them in time. They don't wait for you to pay them later because they have no loyalty. Why should militias be any different? If your region cannot pay anymore, they should ransack your region and take what they can and leave not guard the region forever.
3)Cities being able to support way too many militias
--This is what is causing big issues. Cities were hard to siege before but at least you could starve one years ago. But even then it was still hard to take a city because you still had to deal with militias. Just getting enough siege engines alone take months. To siege a city with lv5 walls, you need at least 50 SEs and even then you will often see siege engines being too crowded. These days, with archers being stronger than the days when you could starve cities, it is nigh impossible to siege a city that is rich enough to put men on the walls constantly. One realm alone can't siege a city that has over 1.5k gold income. You need to bring more realms in just for one city. This encourages realms to gang up on one realm just to take a city. I am pretty sure the game is trying to discourage people from ganging up which it has failed to do so for the entirety of its lifespan. Not saying it is purely the game's fault however since people like to gang up and I don't think mechanics can discourage it. But at least it shouldn't encourage it.
4) With the addition of new market system (--which Anaris is working on to finish but since it is a major change it will take years) and food distribution change (which allows you to run your city at 50% food consumption 24/7 without any major downside), you will never be able to starve a city out. This forces you to the only other option on the table which is siege.
5) Skilled diplomats
They are very hard to come by. Have you checked how many non-warrior class there are in the game at the moment? Not many. There just aren't enough people anymore. You don't even have enough to fight off your enemies. For most small realms, they will hardly have one. Also, skill diplomats only affect relations not actual militias people put in their regions.
