You can fly over the Alps in an hour and land frazzled, or you can take two unhurried days by rail and arrive having watched the mountains change around you. We almost always choose the train.
One route we keep coming back to runs from Munich down to Innsbruck, over the Brenner pass to Bolzano in the heart of the Dolomites, on to Verona and Venice, then a regional train and a bus into Slovenia for Ljubljana and Lake Bled. None of it is fast. That is the whole point.
The practical notes are simple. Favour regional trains over the high-speed ones where you can. They cost less, stop in the small places, and tend to have the better windows. Buy point-to-point tickets unless you are covering real distance, in which case a pass starts to pay off. Travel light, because one bag you can carry up a station staircase changes the feel of the trip.
Break the journey on purpose. Spend a night in a town you would otherwise pass through. Buy lunch from the station market and eat it watching the valleys go by. You arrive a little slower, but you arrive rested, and you have already been on holiday for two days before you reach the door.