All sections are beautiful in their own way. In my opinion, the Oberalp Pass is a highlight, but most of the route is really worth it. I feel that only the tunnels and the areas around Visp/Brig and Chur are less pretty. In all that's perhaps an hour of the total trip. If you don't have the time to do the complete Glacier Express route, just pick the section that is closest to your base town.