I am an active senior who is a first time traveler in Europe. I have a two week period to travel from Prague to Lyon, France (late May, early June), with only one required stop in Bischofszell, Switzerland. Any suggestions for travel (train, bus or air)? Also suggestions for budget accommodations along the way?
Although small budget airlines like Ryan Air, German Wings, and Tui Fly make flying reasonably priced, those airlines usually operate out of smaller airports far from your actual destination and require a car or other transport. Trains will get you closer to where you want to be, often in the center of town, plus, you get the added bonus of seeing some beautiful countryside.
So I'd absolutely take the train. You seem to have the time and it's much more relaxing.
When you plan out your trip and stops along the way, you can find a lot of reasonable lodging that's really quite nice. In Germany and Switzerland, search for "Gasthaus." It's literally a guest house, but often what we would consider a bed and breakfast. They are usually very reasonable and offer great breakfasts. In France, I've used Gites of France to find reasonable, but unique places to stay.
Travel by train is good to maintain budget.