return if $File::Find::dir ne $root_dir;

You're traversing an entire tree even though you ignore all results from subdirectories. Very wasteful! I think the solution is:

sub wanted {
    my ($file)=$_;
    if (-d $file) {
        $File::Find::prune = 1;
        return;
    }

    my $dir_to_make = categorize($file);
    File::Path::make_path($dir_to_make);
    File::Copy::move($file, $dir_to_make);
}
[download]

Error checking would be useful.