I think my point boils down to this: Popular villains often aren’t killed off because they’re profitable and have fan appeal—that’s the real reason. If skilled writers can craft a believable, story-driven explanation for a villain’s survival, I’m all for it. But in most cases (without naming any), the justifications feel like weak mental gymnastics—and not even convincing ones at that.
To avoid straying too far off topic, I’ll say this: I have few, if any, complaints about Star Trek in this regard. For example, it’s easy to accept that the Federation couldn’t destroy the Borg even if they wanted to.