One of the things I've been trying to think of a solution to, is how we can narrow down this issue and determine whether the issue is the ESM or the scripts. As whichever is the culprit is going to require a wildly different approach to trying to diagnose and fix this.
@Mystical Panda has been doing a lot here to point me at the scripts as being the problem- as stack dumps are no good and show me we've got some optimization work to do - but what if the issue is the ESM...
I think I have a really simple experiment to determine that. Would require some folks to run a sacrificial character for a few hours - as your game will be broken from doing this.
Run with the 2.0.0 release of SS2, none of the hotfixes, next download the 1.1.0 patch from nexus but don't install it, grab the ba2 file out of the archive, then use a ba2 extractor to extract the contents of its \scripts\ folder to your Data folder. That will cause SS2 to run with the release esm and assets but the 1.1.0 scripts.
Then just play it for a while building up settlements with plots to see if the long save issue returns at the level you're used to seeing in the 2.0.0 patch.
This will cause plenty of bugs in SS2, but the majority of the plot gameplay loop is unchanged between those two patches, other than checking for incapacitated owners when testing for the plot to be active. So you should be able to build plots OK.
If the long saves return, it points me at the ESM as the more likely culprit, otherwise, I'll be looking at script optimization as our solution. (I plan on doing a heavy optimization pass anyway, as stack dumps should be extremely infrequent - but I'll prioritize it if we're certain its the cause of the long save issue).