It's really hard to make a fair comparison when uGUI isn't out yet, so we can't really fathom the depths of what's in there.
For existing users, something as simple as inertia will keep many in NGUI since that's what they know. Things that I imagine NGUI will have over uGUI, is update frequency, since it's made on the fly all the time, and an update isn't any longer than writing the thing and uploading to a repository. With built in Unity GUI we'll likely have to wait for a "full" update. Conversely, I'd imagine Unity GUI has a bigger and stronger QA department, so you'd assume more of the corner cases have been tested in depth removing the need for as frequent updates.
uGUI has access to the underlying structure of Unity and thus can potentially be faster and get around the quirks that's inherent to being a plugin - as for exactly how much difference there is, that's hard to say right now.
For new users, I'd imagine the $95 mark will be a deterrent, since uGUI finally will have a viable alternative.