It has a target audiance. If you're not a part of it, you might not enjoy it.
HP:Mo R is a deep examination into the illogical workings of the HP-verse, the application of science to the 'verse, and the changes caused by it. It is, essentially, Harry Potter: Let's Have a Renaissance.
If you are not a fan of intellectual discourse, you will not like this. If you want playful student hijinks, the same applies. And if you want your hero to be heroic, mindlessly so, keep looking.
This fic does challenge cannon, a great deal, and in some cases, deliberately alters or ignores it when the sheer illogical stupidity of it gets in the way of the core concept of the story. Professor Quirrel is a central character, and if you know the HP-verse, you can assume what's up with him... except you cannot, because the nature of the story changes everyone involved over time.
The story is also big into the concept of morality as a social construct, and alt!Harry is not the supremely pure good guy many would expect. He does have emotions and they do make him human, sometimes uncomfortably so.
I have seen accusations of Marty Stu, and for a short while, the story feels that way, as the entire thing transitions from the HP-style "Magic is Hard" adventure story to the Mo R-style "Thinking is Hard" moral quandary and mystery.
This story is not a parody, and should not be approached as such. This is not "What if Magic was Science," it is "What if Science came to Magic," which is quite different. Harry enters the magical world with modern sensibilities and advanced knowledge, and sees it for what it is, a backwards and dreadful place that runs exactly like medieval times, with all of the terrible social inhumanities you would expect.
This story is not "fun," beyond a certain point. It is deliberately not-fun, and while it has a fair amount of humor, it tends to be dry, intellectual humor, especially as the series matures. If you read this, read it for the fascinating concept, not to go "Oh, them Weasly's, lulz." If I want that, I can go re-read the originals.
The story is also heavy handed in the intellectual stuff, and that is rather what makes this great. It is written from the view of a highly educated CHILD, and like any such child, it does play out as very heavy handed, deliberately so. Remember, most of the story is filtered through his point of view.
All in all, a great read... IF you are that kind of person.