Hi, first things first : I didn't read all the 39 pages, I'm far of being a dev and my english isn't perfect.
I had the same issue (the first time was the 15th), I first tough I did something wrong (I did not use a glitch or an exploit to duplicate items). I tried everything and I finally started a new V.
Now, I'm lvl 35 with my new V and my save's already >5Mb ... I tried a lot of things I read on reddit or here and you can decrease your sav.dat by a few Kb so ... Useless.
Here's my contribution,
Based on my experience and from what I read, sav.dat get bigger by crafting, looting, doing quests and having the inventory full of (not so) junks.
Increasing the sav.dat limit isn't a good idea because we'll be able to reach that limit.
Possible fixes.
1) Create a .dat file dedicated for almost every sort of action (craft.dat, quests.dat, items.dat, etc.).
2) Purge the save files of unused IDs (as jj284b said).
3) Change save files format to make them lighter
4) Create a "global" file for unchangeable things (like V facegen/voice/lifepath/...)
5) DELETE the dead bodies after a certain amount of time, DELETE vehicles linked to a quest when the quest is done.
I know that I'm far of being the first to have those but here's my ideas.
And I'm convinced that there's no chance I'll be read by a game dev nor a moderator but hey, I like this game and I want it to be better.