Someone over in the zdoom forum made a decent suggestion concerning this.
The idea is an alternate plain-text version-independent savegame format. It would only save upon entering a level or hub. Player's inventory, weapons, health, armor, ammo, etc would be stored, and that's all. This could be tied to an "autosave" routine that automatically saves one of these files whenever a player enters a level or hub, or triggered manually.
These files could be loadable by the command line or console, and probably shouldn't show up as regular savegames (although they could).
While this doesn't completely address the issue, I think it's a pretty good compromise - the player can at least start on the last level he was playing, with the inventory he had when he arrived there.