I think one of the major differences is that NTFS allows you to control file access in a more sophisticated manner. Fat32 doesn't keep track of who created a file, who owns it, or who has permission to read, append, copy, or delete files. Instead you are limited to four attributes (system, hidden, archinve, read only) that are globally applied to all users, and any user can change the attributes of any file, at least as far as the file system is concerned.
I'm sure there are other differences involving limits on file and directory size, cluster size etc. but those are more cosmetic differences, like the differences between Fat16 and Fat32.
Max L.