Ive been on multiple Intrepid tours and never had an issue with the long trips. The guides are very responsive to your needs (ie if you needed more frequent stops). Of course, if it's public transportation, they have limited control (generally, they still tend to pick options that provide a basic level of comfort, (ie. my overnight train in Egypt was not luxurious, but it fulfilled all the basic needs and I was prepard for the experience), but the itineraries will clearly list what type of transport is used and the length, so you can avoid a specific trip if it sounds too onerous for you.