This isn't a problem, so much as feedback. I spent some time crawling thru all the new admin pages making sure I know where everything is located in the new arrangement. One thing was hard to find, and I briefly thought it was gone.
Previously (3.0.x) there were 2 "Sites" pages, both listed in the Super Admin area. Before 3.0 these were labeled "Blogs" and "Sites" (which is clearer). I know that blogs are sites, but having two pages with the same name is confusing.
It makes a little more sense now that there is a "Site Admin" area, and a "Network Admin" area. But, I think maybe these were put in the wrong sections.
Here: Sites Admin: Tools: Sites - you find the "Add Site" section for adding a new site at a top level domain. This is the one I had trouble finding. I was expecting to find it in the Network Admin area.
But what you find here: Network Admin: Sites: Add New - is only the ability to add a new site at a subdomain.
Seems to me these are backwards. Seems like if you're an admin on a single site only, it might be acceptable for you to have the ability to add new sites that are a subdomain of that 1 site (or you shouldn't have the ability to add any new sites at all.)
And as a Super Admin, now Network Admin, you would have the ability to add new sites at new top level domains. Adding new domains is to add them to the network, right? It doesn't make sense as a function for a single site admin.