Direct buses to/from Guayaquil depart hourly for $5 to $8.25. The 3 1/2 hour drive includes a ride over a 4,100-meter mountain pass in El Cajas National Park.
Flights from Guayaquil (GYE) to Cuenca (CUE)
LATAM Airlines Ecuador stops in Quito and then on to Cuenca
2h 55m+ duration
TAME stops in Quito and then on to Cuenca
3h 30m+ duration
Avianca, LATAM Airlines Ecuador stops in Quito and then on to Cuenca
4h 10m+ duration
Hint: I generally find the best deals for seniors by using www.hipmunk.com or any site that has a senior option. Those that do not, chances are you will pay more.