A loot bar counting down while you siege might be an alternative to just getting everything on siege victory. I'll be honest and say that I don't consider looting an important feature though, so it's not high up on my list of priorities.
I cant argue with your priorities and design decisions are your/Pdox decisions, but as Phrox said, I also think that half or more of your points are not really defensible (you can lower amount of loot, explain mechanic, slow down looting units). It WAS possible to improve old system instead of scratching it, ...
My main concern is about the idea that looting must happen at the end of siege. As I was arguing in different thread EU4 is not medieval/early Renaissance game. It encompass also XVIIth century and Napoleonic times, and I am rather happy on my frolic, that Napoleon is not so famous because he was the fastest town sieger in history.
Evolution of fortifications excluded civilian element completely - there was not "treasury room" where feudal lord stored his wealth.
And as density of population rose, most of towns started to become open, as/or their fortifications become obsolete. Majority of means of production/income: mines, plantations, mills, even manufactures were not protected, thus were open to destruction/looting. Towns did not have choice but to comply and pay contributions in cash/food/fodder to marching armies.
Only key strategic points were fortified and modernized, mostly along borders and in capital.
So yes, allies saved Habsburg's asses when Ottomans sieged Vienna in XVIIth century. But did Napoleon siege Vienna? (he captured it twice) In 1805 he entered without even a fight.
And I gave also another example - Silberberg, called Gibraltar of Silesia, build by Prussia to hamper possible Austrian attempt to retake Silesia. Napoleonic troops did not capture it. And so what? Garrison during siege can only defend terrain within range of their cannons. Napolenic armies could live of Silesia almost unhindered.
Paradigm of war did change.
(And if we are talking about early times there is always issue of hordes, which were not interested in storming castles, but enjoyed looting countryside).
System was micro-heavy and maybe unclear, but it could be improved. And IMO it added depth to war. The only valid point is that AI did not do it to player.
Now we have more friendly but less realistic system with limited amount of warfare options. That is design decision but without good background.