Iodine does not kill everything as Aquamira does. At Red Meadows,at Mammoth (yosemite) however, the store only carried iodine.
The SteriPen is convenient because water is ready in one minute or so. However it runs on batteries (the small barrel shaped used in cameras) would be even harder to find at outfitters along the trail.
Along the JMT during the day I used the steripen, purified water in my cooking pot, drank a liter as I sat, and carried no water as I hiked. At camp I filled a three liter platypus, treated it with iodine (since i had not found aquamire at local stores around Yosemite). This would give me enough water for dinner and next morning drinks and breakfast dry milk mix.
For example, I drank water at camp next to a stream below Forester Pass, north side. I carried no water up and over the pass. Drank again at water just below the pass. Carried no water, drank a liter at the next source, etc. Water sources are plentiful right along the trail.
Aquamire is the easiest lightest way to purify water.
Filters are best if your water sources are murky or sandy such as from canyon puddles! Filters are also useful when water sources are scarce from shallow puddles. Flexible plates,(Oraski??) bowls are useful for collecting water from shallow sources. Gravity filters have to be held high up and their bags kept full for the best flows, pumps are less trouble. Shallow mirky water sources should not be an issue on the PCT, but the JMT is my only experience on that trail.
In conclusion, Aquamire would be my choice for the long hike. I have used it along the AT where it readily available at stores along the trail.