Having Save or Die/Suck rules in the game because they aren't really that since there's a proliferation of Raise Dead or Stone To Flesh spells to negate it, is a good example of what we call in improv 'stalling'. You make choices that deliberately or unintentionally delay the story of a scene to deal with preparations of advancing the story of a scene.
If the DM and players are creating/following a story and a bunch of Save or Dies are thrown up to knock off characters... the actual story gets delayed simply to force the PCs to go back to town, negotiate a fee for the spell or scroll, then go back to use it. It's a TTRPG equivalent of a MMO 'corpse run'. Completely unnecessary and delaying of a story simply to give the illusion of deadliness and consequence (plus remove some money from the party's coffers.)
PCs dying should be a story in of itself. It should be important. And that has a much more difficult time of happening when the number of Save or Die effects (plus their "fixing" counterparts) gets higher and higher, because they turn Death into just another condition that the party has to wait for so that it will "wear off".
If the PC dying isn't the important story... don't throw up repetitive roadblocks to the actual one. It'll just bore everyone involved.
I don't view those things as stalling myself. For my games the adventure site which may contain the mentioned challenges is just a part of the story. It just happens to be the part of the story settled with violence. In most cases by being careful or doing research the group can avoid the roadblocks that save or die/suck could present to an unprepared group.
But in the end sometimes the dice fall the wrong way and the group just has a really bad day. I don't really litter my adventure sites with a ton of those abilities but I do use them from time to time as a tool to vary encounters. Its just like traps, if every door is trapped then the value a trap adds to your game is greatly reduced. But I tend to use every tool available to me at one time or another (traps, hordes, environment, riddles, hidden things, queer magical effects, varied monster strategies, etc). While I agree that if your group regularly faces SoD/S encounters they lose their potency and would in fact become an annoyance, I don't want them removed as they can be a great tool to add a little tension to an encounter.
As far as characters dying I agree with you that it should be important. My group has always had a house rule that if a player chooses a course of action that will directly lead to their character dying that they may not be resurrected without the group going to the plane where the soul resides and trying to convince the powers that reside there that the soul that chose willingly to go to their just rewards still has work to do. Because the soul was directly offered by the player. Of course you could devil's advocate me and say that choosing to go into a dungeon is a decision that directly leads to death, but its really not. Its all about intent for my group. Most toons go into dungeons to resolve part of a greater story, or to steal from ugly people. And sometimes in that profession they just have a bad day and they fall in a pit or take a crit to the face and wind up dead. Those toons are eligible for raise magic in my groups games. They still have things left to do so their soul is eager to come back to the prime when the magic calls.
A toon that stays behind to keep a demon lord busy so innocents can escape has directly made a choice to die. Sure the dice could fall in all the right ways and they could live (and that is the stuff that some of the best gaming stories are made of). But really they have chosen to sacrifice their toon for an aspect of the story that is important to them. In those cases I make them play for keeps. I have found that this approach makes the drama of those situations much more personal for my players and it adds history to the game. We have played in the same game world for 15 years and when players sacrifice toons I make the world remember them. Sometimes they will come across some remembrance in the game world of their lost toon (an offering at shrine in honor of the toon, or a statue, in some cases an entire people that views the sacked toon as a hero).
But to be practical with such a house rule you should always warn a player when they are making such decisions that you are going to play for keeps at the time the choice is being made. It lets the player enjoy the drama while choosing the fate of their toon and avoids any misinterpretation you may have about the motives of the player.
Sorry for the long post.
love,
malkav