Reasons Why

Less is More

New system

I don't think there's a need for an intentionally organized and new system like this to solve this problem. I think human society has already evolved the essential features of the solution. Within large units of knowledge, it avoids the problems of inconsistent structure that you mention. What I'm referring to is the common usage of textbooks written by single authors or small groups of them.

The problem is that most of them are not freely available, preventing many people from accessing them and forcing those who can get copies to obtain those produced which much more overhead than would be necessary to download them from the Internet. Therefore, I would say that this is a social problem related to intellectual property laws and social attitudes towards intellectual property.

So imagine that all textbooks were placed online, and that we had a reasonably good search engine for finding them. Let's look at how that would fit your criteria.

Topics broken into modular lessons: The vast variety of textbooks today certainly provides many different separately digestible units of information, both in the separate books and in their separate sections and chapters.

Tree like structure organisation of information: Textbooks' forwards often provide suggested orderings of their chapters, defining a tree structure within the books. There's also an implicit requirement graph between textbooks that isn't too taxing to deduce.

Defining assumptions: Textbook forwards generally also enumerate the assumptions made of readers.

Peer review: Textbooks today are created to be bought by students, based on the choices of this teachers. This sort of market economy is a pretty effective kind of peer review, with the teachers as the peers of the authors.

Lesson specific comments: This is pretty easily grafted onto traditional textbooks in online format. A lot of uses of this would probably be replacements for face-to-face interaction with teachers.

Regular lesson reviews: Textbooks often go through many revisions, reflecting changes in their fields.

Strict editorial guidelines and Funding: These fit in with the market economy I mentioned before, one forced by it and the other enabled by it for successful books.

So, in summary, I'd say that the real problem is building a social structure where potential textbook authors are motivated to release their works for free and where they can hope to survive comfortably despite dedicating large chunks of their time in this way.