I absolutely stopped using MWE and had a huge improvement in the longevity of my characters. We concluded that the problem is related to how MWE handles references and scripts. The scripts that run refer to a specific NPC that is most likely recorded internally in MWE. When the program stops and is restarted, that reference is lost. So the running scripts suddenly have no reference any longer when the game is loaded, which causes a CTD.
MWSE has the exact same problem, but we can take it into account by checking for a reference when the game is loaded again and terminating the script if there is none. Unfortunately development of MWE mods has long been at a standstill.