There's a bit more functionality here than it seems - the 3ds friends list isn't merged/replaced yet but you can *follow* people through 3DS miiverse and they are added to your master list of 1000 IDs that can be followed.
Edit: also it looks like you can make a general post to your own activity feed / friends through the 3DS. It's a workaround for friend messaging to a degree.
I'm curious to know what the update for the StreetPass Mii Plaza does. As far as I can tell, there doesn't seem to be any changes & it appears to be identical.