Having used both, the biggest disadvantage to bar-end is the necessity to move your hand when shifting. Of course, this can be an advantage if you tend to leave your hands on the hoods too much.
Bar-ends have some non-obvious advantages. It's very easy to shift two gears at once. If you're very good, you can even shift 3 gears at once. Or you can "slew" the gears, keeping the shifter one click ahead of the chain position, moving from one end of the cassette to the other. I also found that the bar-end shifter has a more positive feel -- there's a more direct connection between the shifter and the derailer.
Mostly, it's not such a big deal. You get familiar with whatever you are using. Whatever you have, it becomes part of the ride.