FTB comes with DNN out of the box and is easy to configure (only a handfull of options in web.config).
FCKEditor needs to be installed separately (and manually, but there is an installer available at Locopon's) and has many options, a few of them in web.config, but most via UI to be set by an administrator per portal, module or instance.
FTB has additional functions in commercial Pro version - FCK has no pro version, but more functions by default.
FTB does not request users to use right clicks - FCK offers modification options for modifying tables, links, images using right click.
Both editors allow the insertion of DNN images and DNN links (yes, FTB now as well), FCK additionally supports insertion of Flash. The selection dialogs in FTB are more straightforward and easier to user, while FCK allows additional options (many of them I have never used yet).
FCK additionally allows full screen edit and customization of select boxes for styles and formats. AFAIK both editors allow to set the applied css style for editor area, but currently this is not a DNN solution out of the box.