If you are arriving in Guayaquil by air, the bus station is just across the street, so probably just as easy and cost effective if you hop on a bus, as long as you are traveling light and not hauling lots o’baggage with you.
In Quito, you don’t say where you are staying. If you are staying at an airport hotel, they will typically arrange transportation for you. Just send them your flight details and be sure the driver holds up a sign with your name on it.
If you are staying in the city, I’d just grab a taxi at the airport. Should be only about $30 to take you into the city. Be sure to have the address and tel # of your hotel written down, especially if it is one most drivers don’t know.
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