Would it be better to home base in Munich and day trip to Fussen or stay in Fussen and day trip to Munich if you're only considering tax feeling Bavaria by train. Where in each location would be the best place to stay economically that has breakfast?
I think you mean "if you're only considering traveling by train, not "tax feeling" by train. Don't you love those computers that "think" they can correct spelling for you.
If you are only spending two days in Bavaria and day tripping for one day to either Munich of Füssen, then I would say it doesn't really matter much. It's probably more difficult to find an economical place with breakfast in Munich, but it's not that much easier in Füssen, either.
Now, if you have more than two days in Bavaria, I'd advise you to stay in Munich, where there are more things to see and do, and make your one day trip to Füssen.