The value of ethics, traits, and civics, and the Warrior Culture civic

[The Founder]

Well for one, it shouldn't be possible to hold a planet without leaving armies behind. You could implement a system where occupied planets constantly spawn guerilla resistance armies and if the occupiers can't hold the planet the occupation ends. This would make it more difficult to accumulate much warscore against an empire with army bonuses via planet occupation because their guerillas would have those bonuses.

If they just add Unrest from being occupied, that would be done already. For all we know uncountered unrest leads to Rebellions.

Of course all that change does in the end is make the game worse to play for the AI. I said it a few times already and it has not changed thus far:
The Tactical AI can not order new ships or new troops if it needs them. It is entirely dependant on what the Economic AI builds for it based on the budget.

The Admiral AI is going into a war against a enemy it did not choose. With ships it did not design. Armies it did not recruit (and can not order more of). Technology it did not develop. To defend planets it did not build up.

 

[Alliegorical]

you're never going to win a war by retaking planets, you're just going to annoy the hell out of the person you're at war with

it's like stalling a game by building a single house in the middle of a forest at a map edge in the Age of Empires games; you know you have no chance of actually winning, you're just trying to make the other person quit in disgust

Making a losing war too troublesome/expensive for the winners to continue has always been a viable strategy in Paradox games to get a less painful peace deal. For that reason, I rather like Dementor's suggestion; the more planets you occupy, the more each additional planet costs to occupy, until eventually you hit your comfort ceiling and need to end the war with what you've got.