I have tried to find a van/car service between Quito and Cuenca, I did not have any luck with that. There is such a service between Guayaquil and Cuenca, here is their info in case you ever need it: http://www.operazuaytur.com/ , from users reference their service seems to be great.
I love driving in the highlands, but I would not suggest renting a car. The roads are great, but the driving experience is something else, roads and drivers in Ecuador are on the aggressive side, so you better get familiarize before you attempt to drive in Ecuador especially at the mountains sites.
Now, if you would like to have a great sightseeing experience you could try to use the local bus service, you will have to go to the Bus Terminal located in the south end of Quito, purchase a ticket on a walk-in bases, and travel the same day.
The ride could take like 10 to 12 hrs, there is no special bus operator to recommend, you just have to follow your own good perception, and check which one seems to be well establish at the terminal. Some bus companies are Panamericana, Trans Esmeraldas and Flota Imbabura. One way ticket could be around $ 10 US. Best time to travel will be during the day.
You will have watch out for your safety, pack values to carry with you on the bus, and do not accept anything from strangers, specially hand outs on the street, foreigners are always an easy target, just keep an open eye of your surroundings as you would do in any foreign land.
To me the best option to get from Quito to Cuenca it is to fly, www.lan.com is the most trusted airline, on their website you could purchase online and will not have problems along the way, the prices are pretty much standard for airline tickets if you compare with local airline carriers. This option will provide you with the greatest view of the hall canyon seeing from the air, the volcanoes of the Andes. I would say it is the best over view you could ever get of the Andes Mountain on any of the airlines routes in the country.
One last option will be, and if your budget allows it, to hire a Guide + vehicle to take you on the road trip from Quito to Cuenca. Since it is a long distance, 442 Kms + weather conditions may vary; it can become quite expensive, maybe over $ 200 US…
Must travelers look into flying to Quito as your first entry into Ecuador; always look for Guayaquil as an alternative since it is the largest, most commercial and the first port of entry of the country, so you will have a lot more options and cheaper ones to move around the country.
Here I will leave you with some inside views of this paradise name Ecuador,
This maybe an interesting option to travel around Ecuador, here you could check the options they offer…
Get the most out of your trip to Ecuador with a scooter, motorcycle or mountain bike rental from the experts located in Quito, Ecuador…
and some useful links to search for local travel information, not all of them are available in English.