1) Since version 2.9, plugins can now be called through the command line... technically
2) Yes, only a limited number of functions is accessible through the command line interface, but it's because I'm the only one who seems to be willing to add new commands (hum, hum), and I don't have the time / motivation to add all of them as, as you guessed, it's quite some work and I don't personally use the command line!
3) Adding a more generic scripting mechanism (Python, etc.) would be great but would imply indeed a huge work (much more than simply extending the command line tool).
Daniel, CloudCompare admin