1. Lack of integration with CB. Joo!CMS might be a great product, but I am running a site here that relies on CB, I need the forum to be an absolutely integral part of that.
2. Joo!BB runs its own editor, and that has caused big problems with the backend of my site - it somehow conflicts with the native editor, whatever it is, and makes it impossible to edit any forms in the backend. I didn't realise it was a problem until I realised every backend text input field was showing a certain random numerical value, and didn't reflect my edits. I tried the forum solution to fix this, and nothing worked. Since my site > joo!bb, I just switched to another forum solution.
3. Not a great solution if you are looking to import from an existing site - there are no converters available.