Two things personally i would have liked to have seen done differently:
Pluto's involvement in Sailor Moon R - she plays such an important role in the manga and was kind of forgotten in the anime
I would have also liked to have seen the guardians of the Sailor Scouts like in the manga, i thought that was such an important element which was excluded
as for Fan-anime, this may sound wierd but i would love to have seen the backgrounds of the villains. Almost like a spinoff. I think this would have worked really well if this was done with Sailor Stars and Sailor Moon R in particular, like how did galaxia become so powerful? not just "she sealed chaos and its now tainting her body" like actually see her taking over the galaxy (if that makes sense).