It's physically easier (no tiny books deep back sandwiches between large encyclopedias), similar books or books in a series are often the same kind of size (cookbooks are larger, paper back novels are smaller), if you know what the book you want looks like it's very easy to narrow down where it is and it's very easy to put things back/together.

I can understand putting the tall stuff on its own shelf/shelves to save space

Because books come in different sizes, but the number of different sizes is relatively small. So, if the number of books is more than can be fit on one shelf, it most likely makes the most sense to organize by size.

Looks most reasonable. Aesthetically clean lines are pleasing.

I do organize my books by genre (IT/science, high fiction, low fiction, history, non-fiction, language learning).

... and then by size. It's the most aesthetically pleasing for me, genuinely.