1. It's an isekai. The MC is a character from "our world" transported to the game world. In the case of a sci-fi or post apocalyptic setting, I'd assume we'd be talking about suspended animation or time travel or something.
To broaden this concept, I don't think it really matter that it's an isekai or not, specially since in the lore it technically isn't. The "essence" if you will of this point is that it evokes self inserting, you play the role of your character and you interact with that world via that character. It gives you a tabula rasa to make yours instead of giving you a pre defined role and expecting you do play that role.
2. There is some mechanic that stops characters from just killing each other. Or at least massively disincentivises it. Maybe a mental/psychic combat system?
Only relevant in the context of scamtreom and other high tech mediums for wasting money. If it wasn't for dumb guidelines there would be no need for such workarounds. If anything, giving the player the option of killing characters they don't like and having that affect the world would give another layer to the game, as now you can influence the world you're "isekai'd" into a more direct way.
3. There is the ability to transform both the MC and NPCs, physically and mentally. You could probably get away with much less customisation than LT by focusing on meaningful changes rather than tracking the exact diameter of a character's butthole and stuff.
For porn games, butthole diameter is important. In fact, all porn games should give the player exact measurements for butthole diameter of their characters and the NPCs they interact with, preferably
in metric like the civilised people we should strive to be would use.
On the transformation side of things, that's gonna clash with a more structured plot and story. If a character must be a certain way in order to perform their role in that setting, then transforming him in a way that affects that would either make it him character not make sense or require some additional creativity from the writer. Is nice that there is TFs, but how much of it is reasonable to expect?
4. Some similar way of generating sex scenes to LT. Rather than the absurd "fetish" system - where randomly-generated NPCs frequently end up with weird combinations - one could have "personas" for NPCs that make them appear to be people who actually want things.
Or maybe do away with that fetish system entirely and come up with something better, which considering how "good" it is, can't be that much of a hassle.
What you didn't mention is the skills and perks system, though. And those can be interesting if the tree was better designed with more interesting perks. Another game with a similar engine should keep those and maybe take more inspiration from TiTS in this aspect.
Fixing the problems in this game would probably look a lot like ripping the text out and starting over completely with the engine.
How hard would it be to remake the engine...?