After playing with this for a couple of days, I've noticed a few things about how I use it.

First of all, I have a finger-macro (wrist-macro?) for clicking the nav-bar "Newest nodes" link. It takes a bit of mental effort to go down to my personal nodelet and get to the threaded NN prototype. Not really something you can do anything about, though. :-)

Second, I like having both NN interfaces available. When there aren't many new nodes (replies especially), the standard NN interface seems easier to use, as there's less visual clutter to wade through. This'll probably get better when the documentation text at the top goes away, but I doubt that threaded-NN will ever be easier for me to use for small numbers of new nodes than the standard version. On the other hand, the threaded mode is much nicer when I have a lot of new nodes to catch up on, as it's trivial for me to find the threads I'm interested in and ignore those I'm not.

As an added bonus, in Ancestors mode it's easy to not only read a new reply, but read it in context. That's a big win that I didn't really expect, but now that I've discovered it I can't imagine not being able to do it. (What did I do before threaded-NN? It must have sucked.)

I hope this is helpful feedback. Thanks again!