Surprised at my slip of the tongue there with Lynch, and yeah I basically agree with everything you are saying. The guild navigator design is genuinely better (or at least, more interesting) than the book one is, and a lot of the original Dune movie's look could be "2049-ified" to look awesome with modern tech and sensibilities.
And yeah, I don't think Jodorowsky's adaptation would have been a gooo Dune movie, but it probably would have been a good-if-not-amazing movie on its own (like the Starship Trooper's adaptation by Verhoeven...actually wouldn't mind getting a legit modern adaptation of the book).
Probably my biggest concern for the new movie is how much creative freedom Villeneuve has, ideally being near total control. I just don't want them to try and make a "family adventure blockbuster" out of it and dumb down all the subtlety and complex worldbuilding, however the fact that the movie is said to be both Dune and it's sequel gives me hope. Herbert originally planned them both together as the whole DUNE story (as they were released serially I believe in the beginning), and it actually does work better as a "complete" story -- albeit one in two parts -- then just the first book alone, and the direction the narrative in Dune Messiah ends up going, along with the content, are all good signs.
In fact pretty much everything about this movie's production from top-to-bottom thus far has been kinda perfect, enough so that it makes me more nervous than if it was just middling and had lesser expectations. It's so hard to put all the right pieces together to make any movie like this, much less Dune itself, that the likelihood of a "second chance" any time soon whatsoever is widly unlikely.