Should I cancel my Lima - Cusco flight !? Help!

Have you already booked the Inca trail ? In that case, I wouldnt cancel the flight. Your itinerary looks good, giving you 3 full days to acclimatize in Cusco and see its other attractions properly, before the hike.
There are a lot of places that would be worth visiting by bus - but not within your timeframe. Carving 1-2 extra days out of your itinerary, but using 20 hours for sitting on the bus would allow you to see very little on the way, Time is simply too short.
Is there any chance you will have another vacation, later in your life ? Return to Peru later, to visit the rest of the country :-)

A bus trip from Lima to Cusco takes close to 24 hours, without any stops for tourism along the way. Since half of the trip would be at night, you wouldn't even see any scenery looking out the bus windows during those hours. So no, don't cancel your flight. I'm a big fan of bus travel between places in Peru, on almost all routes. But between Cusco and Lima flying makes a lot more sense. It's good that you're planning a proper amount of time to visit Cusco and the Sacred Valley.

Oh, and if you can switch it, take a morning flight to Cusco. The afternoon flights are much more likely to be cancelled if there is bad weather over the Andes mountains.

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