You could fly into NUE if you wanted to. For SkyTeam, both Air France and KLM fly into Nürnberg on regional jets. You'd connect in either CDG (yuck) or Amsterdam, and catch the short flight into NUE on either an AF Embraer 170 or a KLM Fokker 70 / Embraer 170. NUE airport also has a subway train station that would have you in the city center in about 15 minutes. Food for thought.
Why Berlin, if you don't mind my asking? Some may disagree, but Berlin has always seemed somewhat soulless to me.
With your desires, I'd do Nürnberg, Munich and Dresden for 3-4 days each. From Munich, you could get down to Salzburg easily (and cheap if you use the DB Bayern ticket). I stated that Munich's Christmas market isn't all that, but it is still a market and Munich is always a fun town. I spent one night in Dresden last year and wished I'd spent more time. The Christmas market(s) go on forever, and it really is a pretty city. You could also hit Prague from Dresden, and I believe there is a direct rail connection from the Dresden train station.
As for the night trains, I've only done one from Berlin to Zurich on the CityNightLine train about 7 years ago. Very expensive and not much sleep quality. I'd look into low cost flights instead, or maybe a Eurail pass and use the ICE trains.