Use each city for a different part of the trip
Begin in Pristina for the airport and capital, spend two nights in Prizren for the historic centre and fortress, then use Peja for a final town day and a carefully planned Rugova option. Returning from Peja to Pristina is a real travel leg and should remain visible in the last day.
This is a moving itinerary, so choose rooms that make the station transfer manageable. Prizren's old centre is convenient for evenings but not beside the bus station. In Peja, a central room suits the return to Pristina; a mountain guesthouse changes the final-day transport completely.
Decide how ambitious Rugova should be
A gorge viewpoint, village visit and long hike are not the same outing. Confirm transport to the starting point, the route, weather and return. If conditions are poor, use Peja for local heritage and keep the mountain day for another visit. Do not let a guide title promise more than the available daylight permits.
Compare coach and train for the final return
Coaches usually offer more flexibility. Trainkos can be useful when the limited departure fits. Compare the arrival station in Pristina and the onward airport or hotel transfer before choosing. Keep the last night in Pristina if the flight is early.
With four days, omit Peja rather than reducing Prizren to a rushed stop. With three, use Pristina and Prizren only. Add airport travel, mountain transport and guides separately to the example total.