While travelling long distance which is preferable
1) Long flight say 16 hours and shorter transit (3-4hours)
2) or, comparatively short flight(11hours) but long transit (10hours)

I would like to know your experiences.

 long transit is ok if you have a companion with you. 

I prefer long transit to a long flight. I had rather spend time on land than on air. :)

For me, long flight is good if you are travelling on a business or first class. I usually make multiple stops of transit so that I dont have to stay inside the same aircraft and airport for a long time.
When I travel next, I am planning to buy a flight with long transit hours if it's really cheap (i mean like couple of hundred dollars) and use that extra money to book a hotel inside the airport.