When comparing Caja vs nnn, the Slant community recommends nnn for most people. In the question“What are the best Linux file managers?” nnn is ranked 1st while Caja is ranked 12th.
Ranked in these QuestionsQuestion Ranking
Pro Caja script extension makes it more useful
Caja script extension adds your script in script menu, then passes the file name as a parameter. This allows you to run operation which is not included in Caja.
Pro Allows you to access remote or local locations
You can click the Files entry in the panel to access a specific location (remote or local), connect to a certain server (FTP, SFTP, SAMBA, etc.), access your bookmarks, open a new window, as well as to change its default functionality.
Pro Easy to configure
Pro Open or run as administrator in the right-click-menu of the mouse.
Pro It has a reasonable set of features, out of the box
Not too much cluttered, but enough customizable.
Pro Extremely lightweight (55 kb)
Pro Rich set of plugins
Pro Has a great wiki
Pro Minimal configuration with sane defaults
Default options and navigation is simple to grasp.
Pro Unique navigate-as-you-type mode
Pro Awesome new features being added in every release
Pro Integrates with the desktop environment and opens files in the default applications
Save and resume sessions.
Pro Supports cd-on-quit
Allows for quick switching between nnn and the terminal.
Pro Reasonably well-documented
However, it requires some prior knowledge of inner workings of Linux and there are no tutorials (yet). NNN author is making up for this by actively responding to GitHub issues.
Con Frequently very slow to transfer multiple small files
Folders move fine, but it chokes on files, where other browsers take seconds.
Con Mostly unconfigurable
There are not many ways to configure Caja to fit your needs. Besides what can be seen in the settings button you can't configure it further.