The most important differences between them are the quality of buses they have and the cost, which are directly related. Cost differences are minimal, but quality differences are major, and I recommend paying the extra money for the best bus you can find. Another consideration is that with such a long journey, it s best to take an overnight bus, as this will save you the cost of a hotel for a night, and won t waste any daytime. Some lines will accept reservations, and will refuse to sell a traveler tickets without a reservation. One one occasion we went to one of the bus offices and inquired about tickets back to Quito.
Chances are there are plenty of seats on the bus, but persistence is often required.
Customer service is not a common trait in Ecuador like in many first world countries. We paid 7.50 USD each for the 10-hour ride to Coca on one of the nicer buses. It was a large bus that sat about 40 people, with a locked compartment for luggage underneath, and a simple bathroom. The rest of the trip, the driver blared Latin pop music at very high volumes, despite the fact that all of the passengers were trying to sleep as best they could. As morning came, we were no longer surrounded by mountains, but by a lush green combination of swamp and forest.