Hello, new ispconfig look good. I am on SVN last month.
I have few notes:
Separating DBs and DB users is fine, but you should add option to create user with same name as DB in DB add form. Because now I have to go create user in one form and next create db.
I use apache and nginx as reverse proxy. I have to change every time port 80 to 82 in apache-plugin.php. Will be good, if You add some option to define default ports. Method with creating custom VHOST template is working, but it isnt clean, because in apache-plugin is code, which checking if apache is running, but if apache runs on :82 script is think that apache is stoped:
//* Test if apache starts with the new configuration file
$apache_online_status_before_restart = $this->_checkTcp('localhost',82);
//* Check if apache restarted successfully if it was online before
$apache_online_status_after_restart = $this->_checkTcp('localhost',82);