When I was working there were times during rush hour when not only was every seat on the train taken, there wasn't any standing room, and I got left behind. Of course, avoid rush hour on trains out of downtown Zürich and Bern just before a holiday, and you'll be fine.

I travel mostly 1st class these days, for the higher likelihood of it being quiet. That said, 2nd class really isn't so bad, and if you're traveling short distances, it's fine.

The nice part of staying in Luzern, is that there are direct trains to the airport. It's a nice ride as well. You're also quickly in Ticino, or Como, or even Milan. Usually if the weather is bad in the north, it's good in the south. But you are indeed on the eastern side.