First I must say that I watched only the avi version (not the 1.3 DVD release)
Like Nishit_Singh the Stan Bush songs at the end bugged me.
A lot of crap is gone which is good. However some crappy things are still there (Sam’s mother, the kitchen robots, the twins, Leo). But maybe it’s not possible to remove more without creating continuity errors.
To be perfectly honest, I don’t really think those things are the real problem of the film. To some extend those things can be fun!
In my opinion the film problem is simply too long! At some point Egypt I couldn’t stand watching the movie anymore. I had to force myself to stay till the end both with the original and the fanedit (even more with the original since it is longer).
Maybe there’s a way to cut all the things that are not essential to the story to make the movie shorter.