I am planning my next visit to Ecuador which will include visits from Quito to Cotacachi, Cuneca and Manta.
I can not find direct flights from Manta to Cuenca or vice versa. All flights seem to go through Quito. Does any airline fly directly between Manta and Cuenca?
Short of chartering a private plane, there is not a way to fly directly from Manta to Cuenca. You would have to change planes in Quito.
On that subject, you should know that lately the airline TAME has been cancelling flights, sometimes at the last minute. If you can, using Avianca/Aerogal and/or Latam may be best.