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Choosing between Salta and San Salvador de Jujuy does not require deciding which city is better. The useful question is what you want to do after arrival and how many transfers you are willing to add. A convenient flight can lose its appeal if it requires crossing the region again at the end. A well-placed base can reduce movements without being the city with the longest activity list.
Look at the whole outline
If the Quebrada de Humahuaca is the focus, first place the nights you want to spend there and then compare arrival options. If Cafayate, Cachi, and Salta city dominate, sketch that group before adding Jujuy. These are ways to organize interests, not boundaries preventing a trip across provincial lines.
Include the departure in the same outline. Compare arriving and leaving through one city with using different cities, checking transportation, rentals, and possible return charges. Do not assume a vehicle can be returned anywhere or that a direct connection will operate when you need it.
A first night with fewer dependencies
After a long journey, a night near services may be more useful than covering the greatest possible distance. Check how to reach your accommodation if the flight is delayed, when guests can check in, and where you could eat. A low room rate loses some value when it requires several uncertain connections with luggage.
Treat the airport, bus terminal, and city center as separate points in your calculation. Sharing a city name does not mean sharing a location. Request a quote for the actual transfer, including passengers and luggage, and save the full accommodation address offline.
Compare without making arrival a race
Draft two short versions of the trip using the same priorities. Note each overnight stop, every essential transfer, and which visit would be omitted in each version. This reveals differences more clearly than counting attractions or looking for a universal answer.
Choose the option that retains some margin when something runs late. The arrival city can be a worthwhile visit in its own right. Reserving a morning to explore it avoids treating it merely as a waiting room between the plane and the road.