I have alternated between flat and drop bars and much prefer using drops because it is an easy transition between the touring bike and the road bike that I ride most. If on the other hand I rode a mountain bike more often I might prefer the flat bar for that reason.
However since my touring bike is full XT-XTR I think that the Rapid Fire shifters and brake levers, overall, work better than any drop bar combinations I have tried, albeit a heavier solution.
The flat bar setup does offer some advantages though. First cable replacement and adjustments are much easier. Second flat bars offer a good storage area for spare spokes, cable ties etc. Third for boxing up the flat bars seem easier for me.

BTW switching between flat and drop bars you need different stem lengths to set the bar ends and brake hoods at the same riding position.