Stops are not a problem. Japan's Shinkansen has exactly the same problem of prefectures/municipalities forcing railways to build a station in the middle of nowh

Stops are not a problem. Japan's Shinkansen has exactly the same problem of prefectures/municipalities forcing railways to build a station in the middle of nowhere. There are literally dozens of such stations even on the busiest routes. The solution is simple: most trains don't stop at these station and pass them at near max speed. There are special "slow" trains that stop at each station and timed so that they get bypassed by quicker ones.