FBReader uses a non-standard method for programs to ask it to open books via its plugins, which is why CC can't see it and doesn't propose it. It is also why the two file managers I have don't propose FBReader for pdf files. I really wish that developers wouldn't make up new "standards" for common things.
At any rate, I figured out how to launch FBReader on a pdf and while at it, on djvu, and added special code to CC to handle these two cases. It will be in the next release, perhaps the end of this week.