Thinking on it more, what makes me kind of angry about the ending is that there's no logical reason why someone would design the Neo World Program to work the way it does.
I mean, at first it kind of makes sense- the characters are basically themselves minus their memories after entering high school moved (rather than copied) into the system, and upon graduation they're meant to overwrite their old fucked up personas in the real world. The characters who die have their data deleted, and their real bodies can't function without having something written back to their brains by the system. Junko plans on exploiting this by writing herself over the brains of the dead characters instead.
But then the shutdown thing comes up. Now they say that if the whole program just shuts down outright the living characters will wake up and be just as they were before they were hooked into the Neo World Program, forgetting everything that transpired inside... but the characters who died stay dead.
This doesn't make any sense- if the reason why the dead characters couldn't wake up is because they needed the data the Neo World Program was supposed to return, then that should apply to the living characters and mean that they can't wake up after the shutdown either. If the only consequence of the shutdown is that they all revert to their pre-Neo World Program states rather than (mentally, at least) becoming who they were after graduation, that should apply to the characters who died in there too and they should have woken up after the shutdown just like everyone else.
Beyond that- why the fuck would you make a VR program of any kind that had the potential for real-world consequences if anything went wrong inside the VR world, unless your whole intent was for it to be a deathtrap (such as in Sword Art Online)? I mean, I get that the Junko-virus wasn't something they expected, but there still could have been bugs, accidental deaths, etc.
It just feels like the whole reason why the tech works the way it does is because that's how it has to work to make the game sufficiently tragic. I get that the writers wanted to have their cake and eat it too in that they wanted the "it was all virtual realty" twist but didn't want to invalidate all of the deaths that happened in the process, it just feels like they could have gone about it better.