I do not dispute all of Ebert's points. It's true, it failed to convey the story correctly. I still wonder where he got the idea that Paul looked like he was surfing the worms, and that the worms looked like Kermit. He occasionally comes up with weird interpretations, but he is definitely an foremost expert on film. Maybe the film could have been remedied by cutting out all the unnecessary stuff, therefore Lynch would have had a stable script to work with, and be able to employ his strengths from his previous films to enhance the story. I'm surprised that Lynch didn't do his own special effects, because he's done some impressively weird and convincing stuff on his own in ERASERHEAD (not that it would have improved the film).
Unless we forget, de Laurentis may share some of the blame for the film's effects. The guy seemed so into campy Italian monster and sci-fi movies for some reason, I guess because they had pizzazz in his mind. The funny thing about Flash Gordon: de Laurentis wanted to make the movie as a response to Star Wars, which he disliked, and couldn't understand what audiences loved about it. Little did he know, that Star Wars borrowed a lot of elements from the original Flash Gordon serials, and that SW was meant as GL's own tribute to FG. I guess Laurentis didn't think SW had enough pizzazz as a space opera, nor Italian enough

I have to admit, I love the Weirding Modules. They're not in the book, but I like how damn effective they are as weapons. It would have been nice to be true to the Weirding Way, but de Laurentis and Lynch didn't have the benefit of Bruce Lee as a choreographer. Could you imagine the Kyle Maclachlan attempting to fight like he was in Fist of Fury? Thufir would have be outraged.