This is not exactly worpdress multisite suggestion, but a hack to run and manage multiple wordpress websites. I don't know if it works for you :
Create one database for each of your site and create a connection to corresponding site by placing wp-config.php inside the site1-content etc folder. You would have to point all your domains to root folder. Make some modifications in wp-load.php to connect to appropriate database depending upon requested URL. You may have to create a common database as well to save this connections. (Not a difficult job to do though)
Now your folder structure would look like :
- common > wp-admin
- common > wp-includes
- common > must-use
- other core files normally on root
- wp-config.php(with database connection to site1)
- wp-config.php(with database connection of site2)
Now you have multiple wordpress websites which are using
- common wp-admin folder, wp-includes folder - therefore making up gradation with word press easier and centralized
- common mu-plugins folder to ensure all the sites have this common required plugins up and running. Again with centralized up gradation possibility
- Of-course this are multiple word-press websites not word-press multisite, therefore independent user base.
- If you dont want to create multiple database you can use different table prefix for different clients (defined in wp-config.php) and make appropriate connection depending upon the requested url
Difference of above solution from multisite :
1. wp-content folder is different for each of the client Though you can make plugins and themes folder same by moving it in the common folder ( using wp-config.php)
2. You can network activate plugins by placing it in must-use plugin folder inside common folder.
This does solve your maintenance problem and up gradation path easy for all the website. Though you would not have access to awesome super admin tools available in wordpress multisite. But you do have different requirement as well.