Pluto's atmosphere has been studied since the 1980s, using spectroscopy and stellar occultation (watching starlight flicker as Pluto passed in front of it). It wasn't a surprise when New Horizons observed it.
I wasn’t thinking about the atmosphere. I meant in general, Pluto surprised more than other first fly-bys. Uranus is obviously extra weird in a lot of ways but who was expecting Pluto to be as interesting?