I want to say I mentioned this before but I think the reason that there are issues is in deciding who the 'attacker' is. The war goal is part of the defenders territory.
I wonder if it would be better when you declare independence directly that if your liege doesn't acquiesce they become the 'attacker' and you the defender (as if you are free and they are reclaiming the territory). I think it would fit better.
When there is an independence faction I wonder if it would be better served if it was multiple wars or splittable by general area. That way Bob, who is on the other side of the world doesn't lose you the war because his land was recaptured while everyone else is doing well. Maybe all defenders are solo wars but a way to join others wars as allies? I have not thought the faction part all the way through.
Yes there are other wars between liege and vassal, when the vassal is the attacker for no reason, and have to siege the liege capital, and it makes no sense at all. Just 2 examples:
1- Liege: "Ey vassal, i want you to convert religion". Vassal: "No way". Liege: "Ok then i will arrest you". Vassal: "Ok, come to my land and get me if you can, i am going to fortify in my castle, and the only way you get me is if you conquer it".
How is that it is the vassal who has to conquer the lieges capital!? No sense.
2- Liege: "Ey my dear vassal, i am going to confiscate this county, i want it for myself, give it to me!". Vassal: "No way". Liege: "Ok then, i will take it from you by force". Vassal: "Ok, i am waiting for you, come and take it if you can".
How in the hell is the vassal the attacker, and why does he/she need to conquer the lieges capital?! Instead, it is the liege attacking to take a county by force, and it should be the liege who needs to conquer the land to get it. No sense, again.
Just 2 examples, but there are plenty. I hope they rework a bit this part of the game, because right now too many things are ridiculous.