The Hyperion cantos (Simmons) is sadly not taken seriously by very many authors of top-100 lists. It's usually Dune or Stranger in a Strange Land or Ender's Game or Forever War. And heaven forbid they include Neuromancer or Snow Crash or Altered Carbon, or an eco-scifi book like Stand on Zanzibar or Zodiac.
Dune could be a nod to the classic science fiction aficionados who don't care for any of the newer stuff, who love Asimov, Niven, Clarke, PKD, Bester. Is Heinlein too politically charged, perhaps?
It sounds like you heard the Endymion pair are rubbish and avoided reading them. Wherever you heard that, they're not. Look at the ratings on goodreads[1], for instance. You're talking about them as if the Endymion volumes fell off a cliff like Vinge did with Children of the Sky[2]. Not so. The amazon ratings distribution for Endymion is a bit lackluster compared to the other volumes, but still nothing that could be called "rubbish".
[1] https://www.goodreads.com/search?utf8=%E2%9C%93&query=hyperi...
[2] https://www.goodreads.com/search?utf8=%E2%9C%93&query=zones+...
And you're right, it's a great book and does not deserve to be pigeonholed into some niche category.
Actually, Vinge's True Names would be top on my list (and only 90 pages or so).
The Handmaid's Tale is far better, but is listed as "Feminist Speculative Fiction"; if I'd read the category first, I would have skipped the book, but the book is great, along with her other writing.
In a list of 100, I'd probably include 3. The Handmaid's Tale is fine; Snow Crash or maybe a Heinlein or a "golden age of sci-fi" choice.
(Edited to fix incorrect title, thanks)