Hi, I like ee very much for as much as I have played with it for a while.
However I have a security concern: all the files are owned by www-data which means that they are writable by the server. That is not a good idea as any small vulnerability can lead to complete controll over the code, and that not only for one site but for all the sites on the server.
I will personally change the owner of the htdocs directory and it’s subdirs, but it would be nice to have a possibility to chose an owner at the moment of creation of the site.
Also this way, you wouldnt have to run wp-cli as root for further site management.