When comparing Caja vs Nautilus (AKA Gnome Files), the Slant community recommends Nautilus (AKA Gnome Files) for most people. In the question“What are the best GUI file managers for UNIX-like systems?” Nautilus (AKA Gnome Files) is ranked 9th while Caja is ranked 10th. The most important reason people chose Nautilus (AKA Gnome Files) is:
On recent versions of GNOME, you can click the Files entry in the panel to access the 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.
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Pros
Pro Easy to configure
Pro It has a reasonable set of features, out of the box
Not too much cluttered, but enough customizable.
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 Open or run as administrator in the right-click-menu of the mouse
Pro It just works
Customizable and clean, this is crushing that garbage nautilus, the overrated p.o.s. gnome destroyed.
Pro Allows you to access remote or local locations
On recent versions of GNOME, you can click the Files entry in the panel to access the 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 Widely supported
The program is distributed as a single source archive, which can be configured, compiled and installed on almost any Linux flavor. There are no binary files for a specific Linux distribution, but you can install it directly from the default software channels of your operating system.
Pro Google drive integration
Pro Easy to use and familiar user interface for Ubuntu users
The user interface of Files is very familiar to Ubuntu users, most probably because Canonical still uses Nautilus (an old version of it) as the default file manager for its world’s most popular free operating system, Ubuntu Linux.
It split into two parts, a sidebar and the main file viewer. While you already know what the latter can do for you, the sidebar offers quick access to Places, Devices and Network locations, as well as any other bookmarks that you can add whenever you want.
Pro Convenient file moving progress
Nautilus shows the progress of file move operations in the top right. This doesn't get in your way. You can keep using the window while the operation is progressing.

Pro Fully supports DPI
Cons
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.
Con Sort Order / Limited Configuration Options
It ignores special characters when sorting files and folders. Underscore, tilde, bracket, ASCII characters, .... everthing not recognized in numeric/alpha sorting. Also, I found no way to remove the triangle to reveal contents of sub-folders rather than opening... but I did quit looking after several seemly unalterable functionality issues.
Con Very slow to list thousands of files
Unusably so.

Con Mostly unconfigurable
There are not many ways to configure Nautilus to fit your needs. Besides what can be seen in the settings button you can't configure it further.
Con Gradually losing its features
Unlike most software, where new features are added over time, Nautilus (along with other Gnome applications) tends to lose features, and for unclear reasons.
Con Doesn't support "open as root"
Con No Tree View option any more
This is a crucial feature for my daily work with a file manager and without a Tree View option a file manager seems pointless to me.
The reason for dropping this feature is weird. Quoted from here:
"It is the list view after all. Tree models don't work well on
touch and it isn't consistent with the file chooser."
Con Slow
Seems to be one of few file managers that can take several seconds to open.
Con Comes with a ton of dependencies
