Cadfan, thanks for the insightful & well-thought-out post!
In 1e, players were not automatically allowed to choose optimal spells as they progressed in power. It therefore made sense that NPCs would not have optimal spells, either. This set-up made it quite a bit more believeable that SoD spells could be rare. Likewise, in 1e, you didn't have the "obnoxious chore" of casting the applicable ward because it didn't exist.
But that doesn't address your main point.
I agree that SoD effects should be rare. Most things that are SoD in the game right now would be better dealt with as a "Save or Increasing Effect"....such as increasing DEX damage indicating that the character is slowly being turned into stone. Perhaps the character should gain 1 Hardness and take 1d6 DEX damage per round until petrified. There could then be methods to halt or reverse the damage done.
Anything that increases meaningful decision making in a campaign is golden, IMHO.
As far as level drain goes, if the game decouples skill points and feats from level as an absolute, you can have level drain affect only BAB, HP, Saves, and Spells. Have it affect only the spells you can cast, and not the spells you know or have memorized. For example, if you have two 6th level spells memorized, and level drain causes you to be able to cast only one, you select the one you can cast at the time you cast it. This greatly reduces bookkeeping.
OTOH, I absolutely believe that SoD is appropriate under certain circumstances. The save in Coup de Grace, for example, is a good idea. Likewise, a campaign can benefit from having monsters that the PCs know to exist (and likely know where) that have SoD effects. Many of these could be written using the "Save or Effect" mechanic, though....If the Mother of All Medusas does 20d6 Dex damage per round with her petrification (save for half) that is the same as a SoD effect (or worse!) for all practical purposes.
Finally, I think that (barring magic) some things ought to simply kill you (ex. immersion in lava). In these cases, a save represents the event
not happening (i.e., you catch the lip of the pit, etc.) rather than you ability to "tough it out".
IMHO, of course.
RC