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.

http://www.elegantthemes.com/blog/tips-tricks/how-to-manage-multiple-wordpress-websites-effectively

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?