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This concern has been raised several times and needs to be looked into. If it’s not necessary for you that doesn’t mean that it’s not necessary for the next person, most especially now that we are seeing the rise of WAAS with wordpress. There are several people currently using the WP Ultimo to sell websites with wordpress multisite. Does it really look professional having all their client sites share the same users, even if that user did not register to other sites?
Individual user and user_meta tables for each subsite!!! The good thing about this is that if super admins use the same user login and password across all the sites, they still maintain their super admin privileges on each site and are automatically logged in when switching sites and can easily manipulate any site on the network.
Subsites users can be able to use the same email with any password on each site on the network not knowing that those sites are related. A layout was set here: https://core.trac.wordpress.org/ticket/15467. This can be improved or modified, as the code currently has several defects, eg: you have to add users to subsites user and user_meta tables through sql queries or phpmyadmin, subsites users authentication is currently not working properly ect.
Subsites separate user authentication could be done with just the check of a box for networks that want the feature. Please wordpress developers… If you see no other reasons to look into this just consider the fact that there are people like me out there who want to use wordpress to provide Websites As A Service and host client sites.