I think a huge part of how people read your post is that you entitle it "Werewolf 2.0's Nine Design Flaws and how I would fix them" but you then go on to say, "this works fine in tabletop but not on MUs".
That´s false advertising, bro. Say what you mean and mean what you say.
"What I Think Doesn't Work About Werewolf 2.0 On MUs and How I Would Fix It" would be a better title.
It's also making me roll my eyes whenever you say '[my way] would be [more] WoD-y than the current". You don't really get to decide that, and in fact, it's blatantly false.
I also think that your claims that the Shadow/Loci/Harmony have never been done well on a MU isn't really a reason to do away with them. It's a reason to look at new ways of doing it.
Personally, I love the Shadow, spirits, etc. It's part of what draws me to the game. If it was just generic werewolves? I might play, but it wouldn't draw me the same way. Does it mean it has to be the focus of every story? Absolutely not.
I like Loci. They are an integral part of the setting because they marry territoriality with the Shadow. They are the link between the two, and should be important. Does it mean it has to be the focus of every story? Absolutely not.
I love Harmony, especially in 2.0 -- the internal struggle between Flesh and Spirit makes me grin because I can see how my character would fight for balance, but how their character flaws will make that a challenge. Does it mean it has to be the focus of every story? Absolutely not.
But I really like these aspects. I love Auspices. They are evocative and help design purpose in your character. I love Tribes, they are different cultures within a larger one, ways of thinking rather than being [Auspices].
I could go on. In the end, it's all about preference. You can absolutely excise all this stuff and still have an enjoyable game--but it is not WoD Werewolf. It just isn't recognizable as such.