Multisite vs services like InfiniteWP and how to manage multiple unique sites efficiently

I keep getting hung up on the limitations of multisite environments. I had originally installed it to make the administration of multiple sites easier. But with its user management system being dependent on the root site, I am unable to keep these multiple sites separate in an efficient way. I have been over these forums a million times looking for a solid solution to that issue but there seems to be nothing comprehensive out there. I came across InfiniteWP and I'm wondering if anyone out there has tried it and prefers it over multisite for the administration of multiple wp sites.

It sounds weird to even write that multisite does not actually work for multiple sites but its true. Multisite should be renamed to megasite because it does not do a good job of actually administering multiple unique websites.

Has anyone else ran into the same problem and found a solution?