We need to get from Berlin to Munich in mid-April (we fly home out of Munich). I had planned to take the train but am wondering whether we should fly AirBerlin in order to save a bit of time (the train trip is almost 6 hours). Is it a scenic train ride? I also know that sometimes flying doesn't save that much time because of having to get to the airport early etc. etc. Another possibility is to tweak our itinerary and stop somewhere for one night between Berlin and Munich. Any opinions?

What's wrong with a six hour train ride? It's not that long, and you'll enjoy more freedom than being crammed on a plane, you can get up and walk around whenever you like, have lunch or a drink in the restaurant car etc. The train takes you from the very heart of one city to the very heart of the other, so you won't save that much time flying. Besides, there is the aspect of pollution.

Scenic ride - well, not spectacular, but there are some pretty parts (depending which route you are taking), and you'll get a good impression of the different German landscapes, the plains of the North, the hilly center and South, the rivers and valleys.

If you want a stopover halfway, I'd suggest Bamberg.

Admittedly I am not a happy flyer, but I would always take a train over a plane, especially in Germany when you have the option to ride the wonderful ICE trains. Assuming the DB and associated staff have gotten the strike bug out of their systems, the train ride should be smooth and will be less prone to weather issues (fog problems, for example).
The 9 am (well, 8:58) ICE whizzes you down to Munich in 5 hours, 41 minutes and flying wouldn't be that much faster, when you factor in getting to from the airport, check-in time, etc. Nuremberg is one of the stops on the ICE from Berlin to Munich and it's worth an overnight visit.
Bamberg is also a great idea if you want to stop over; there are direct trains from Berlin to there as well and it would be nice to have a small city in between two large ones. I like Nuremberg, but Bamberg is undeniably prettier and more charming.

Thanks for the replies. I'd much rather take a train as well so I'll probably stick to my original plan. I find it much more relaxing--no worries about lost luggage etc.

Take the train. I was very impressed with the system and it is a pretty view along the way.