@googolplexbyte
The only point you made that is both usable and abuseproof is the one about Direct Replies, adding it would reduce the mess that is trying to respond/interact in the current system.
Upvoting and downvoting, just like using soft bans and adding a reputation system will only create an echochamber due to how easily they can all be abused, this is something that can easily be seen on Reddit, where anyone with a different opinion gets downvoted into absolute oblivion.
About the comment order, wouldn't it make more sense if the most recent comments came first? That way it would take less time and effort to find recent comments about the manga, helping the users decide if they want or not to read it. Also, what's a "positive" commenter? Besides, one shouldn't follow the lead of others, we all have the right to see the good, the bad and the ugly about everything and, using that as a basis, decide our own perspectives and positions. I'm not saying those who say shit should be favoured, I'm saying that no one should be favored, one with sound arguments naturally will conquer the attention of the readers. A system like what you suggested is something prone to being abused and being used to make an echochamber.
Now, regarding all you said about positivity, are you trying to directly control what people can feel and express? I'm kinda tired of everyone saying that things sound too Orwellian but hell, this
is Orwellian. Adding that with the reputation points and the clear tag saying who's being a bad boy is just like the Social Credit System of a certain country on Asia and pretty much all the way into tyranny you could go without explicitly saying "Let's ban those who aren't positive!".
Finishing this with a bit of wisdom:
Forced positivity isn't happiness, it is an incubator for hatred.