I don't like
intending to change the rules of the game from the get-go.
I think it would betray the idea of "Naruto figuring out the game", and more importantly, I think it would make it more confusing for the reader. (Having other people involved is a super-serious issue I'll address in like two paragraphs).
Also, there's no need for something like "optional bosses" or "DLC" when there's a whole entire world being "simulated".
If you want to do something different, take different missions.
If you just want to fight someone without worrying about consequences at all, go tell the Raikage his leadership is bad and he should feel bad.
also
The idea of Kakashi running it made me realize the perfect candidate... so the "hint corner" after Bad Ends will be called,
"Obito's Graveyard". He'll be a different kind of undead every time, like a ghost, and a zombie, and a mummy, and a vampire... maybe later there will be cameos from other dead folks.
PvP, getting PMs from admins, etc
I think this complicates the premise too much.
Classically, there are three kinds of conflict in literature (complete with a historical artifact of implicitly sexist language):
1) Man vs. Man
2) Man vs. Environment
3) Man vs. Himself
This concept is firmly rooted in the second: Naruto isn't really struggling against other people any more, he's trying to beat a system. Pulling other people into that contradicts that fundamental premise, and pushes it back towards the first (Man vs Man).
Having other people be players,
especially having him deal with "admins"; once those come into play, you'll have Naruto calling them out like this:
Naruto: Why the fuck are we all trapped in a suffering simulator!?
Once the "game" stops being some inscrutable vast machine, once it stops being "the laws of reality" and starts being "a constructed place", then Naruto will be in a position to call all the programmers assholes for trapping him (and possibly others) in a simulated reality where there is no apparent reason for anyone to fight and die and suffer.
The "game" has to be a different "physics ruleset" than he's used to; it has to be "the unthinking universe", because otherwise....
Once Naruto is telling the Matrix to eat a dick, we're talking about a
much different kind of story.
That's a full Cerberus Shift. I'm not saying that would be a bad story, but the fundamental implications are much darker than I think the people suggesting these things fully realize.
Best case scenario is, he's Tsukasa from the first dothack anime, only he
also has amnesia, in addition to being in a cybercoma. The ending is either: he rejects reality and stays in the illusion, which is the opposite of Naruto,
or he wakes up and he's just some dumb kid without any special powers and abilities and he's two years behind in school, and he's gonna go live a normal life now. (And he's actually a girl, and Hinata's in a wheelchair).
Worst case...off the top of my head.... The Machine Empire drinks chakra for fuel, and experiments have shown ninja wars produce the most chakra, so the Matrix is designed for unceasing chakra-user violence. Tobi's the hero because he's going to full Kobayashi Maru the crap out of the Matrix by using the Moon-Eye Plan to instantly close the chakra tap overnight and crash the Machines' energy infrastructure.
At any rate, once other people start participating, that effectively ends the "Naruto the Video Game" story and forces it into some kind of cyberpunk. I'm a big fan of scifi but that's not what I want to do here.