Now that is just a failing in most ebooks. Calibre has fields for series name and sequence and I wish that the my eReader had the same. It seems quite easy, actually.
I was also thinking that an omnibus would be an easy way for publishers to give discounts when someone buys a whole series at once without having to rely on the bookseller websites to provide the functionality. But I'd bet that stuff like that is just a reflection of the immaturity of the ebook marketplace.