Battery life is a significant issue. My Garmin 305 watch will run all day, but it must be recharged. A typical handheld unit takes AA batteries. I took my eTrex Vista Cx on the entire JMT and only changed batteries a couple of times.
I find the watch to be convenient and the handheld to be more useful overall. I use both at different times. Generally, I am not using the GPS extensively for navigation and opt for the watch as being easier to deal with.
I do not have an iPhone but was not impressed with friends' experiences. As I understand it, the phone uses cell towers when possible in order to save battery life. There is a GPS receiver chip, but it drains the battery quickly. As a stand-alone GPS unit, it did not look great to me.