There is huge room for improvement in the process of creating and managing users and sites in WordPress, especially where MultiSite is concerned. I put together a whole long term look here: http://martythornley.com/2013/08/multisite-improvement-ideas/
But to start the signup and login process should be looked at.
There is inconsistency and overlap between the processes of a user signup for a single site, a user signing up for multisite ( as a user ), and a user signing up for a site within multisite.
To make things more confusing the process of a super admin creating users and sites is different as well. This makes it very difficult and in some cases impossible for a plugin to simply add a field to new users, like a phone number, for example.