In the case of Neuromancer, I liked the book a lot when rereading it but thought the story was completely incomprehensible when I read it for that class...I couldn't follow it or knew what anything was to save my life. The nova and concepts were sort of impressive but I really had no idea what the characters were even trying to do. I understood the story a lot better on re-read, but that was with it still being hard to follow.
The other problem of course is that just about every other William Gibson book I read had the same problem, only I knew re-reading them wouldn't work like it did with Neuromancer.
Regarding your analogy, you're probably right; in particular, I suppose the "navigating data" stuff is the most dated and would probably just end up being what, CGI of futuristic vehicles travelling through fields of ones and zeros?
Matrix sequels: the first one is one of the most spectacularly overloaded boggles ever filmed and the third is just a video gameish action climax to the second. I feel sort of bad for the Wachowski...er, brothers? sisters now, I guess, who kept making these ambitious films that ended up with little shelf life; they're like the poster kids for that stuff.