I think what's key with regards to to recurring characters like Puzz and Trowzer is the presentation and world-building aspect. It's not that they have to go the route of Banjo-Kazooie, but something other than the characters just sort of standing there. Mario Galaxy, for example, had the Captain Toad crew appear in many levels -- rather than always in the ship, they were often interacting with the environment in some way (exploring, repairing their ship, in danger, etc) ... and they would have their own theme music when you spoke to them, also.
What we've seen is reportedly round abouts two months old build and it wasn't long ago they were still considering an October release. I'm sure they think about how they'll present the characters and make them feel alive within the game's world. What *little* we've seen of Dr. Puzz in the first two worlds doesn't seem to achieve this at the same level Banjo did (same pose/set-up in both worlds ... less presentation doesn't excite, dialogue aside) but there's much we haven't seen and it's all in progress!
I would agree that I hope to hear some more character-specific themes!!