From what I’ve seen so far, I don’t think you need to worry about folder structure. I point my movies library at the root of my Full Movies folder. Within that, I have several hundred loose movies, and a few dozen folders. These folders are for when a series has 3 or more movies in it, or if the movies in the series don’t stick together alphabetically (hi, DaVinci Code trilogy!). Plex has no problem drilling down into sub folders regardless of its name, so I don’t think you need to repeat the movie year in the folder name.
UNLESS you are going to include special features, vignettes, trailers, external subtitle files, etc for each movie. In which case… I don’t know. Maybe it’s necessary for the folder to match the movie file name. Perhaps someone with more experience with that may help.
As for doing what you are doing with Batman, that’s fine. Depending on WHERE you have these files named like that, my advice changes:
File Structure: If you want to keep movies grouped up on the server, and have Plex detect them, it will work. I would advise you to add them all to your server at a different time than the rest of your videos (this is so it can be easy to see newly added files). If a file is named Batman 03 - Batman Returns (1992).EXT then it might or might not get picked up properly by Plex. Thankfully, you can easily Fix Match or manually match the video to the correct one, and that match will stick. The name within Plex, however, will pre-fill the title field with the proper title: Batman Returns.
Plex library: If you want the movie in your Plex library to look like this, you can here as well. Once the movie has been added to Plex, you can Edit (pencil icon) to manually change the title of the movie. Plex will respect the title change, and sort it in the library based on that title. I do this for my Scooby Doo TV Shows, labelling them Scooby Doo (YEAR) - SHOW TITLE. This arranges all the shows together, and is then listed in order of release date. It should (and does) work the same way for movies.
A good alternative to the above option, though, is the use of collections. You can have Plex “collect” these movies together automatically, or manually make a collection and add movies to this grouping. Then, when you look at a collection, the movies in there will automatically sort by release date by default, but you can change that to a manual sort if you feel like sorting by… I dunno, duration. If you use a collection, you may not need to change the title of each of your batman movies, since when looking at the collection the movies will be sorted for you.
