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The iPhone app & the desktop sync, so the system is "one trusted system". While the iPhone app is great for it's use of location based contexts, there are some things missing in it, that only the desktop provides. For example:

Review: GTD suggests a weekly review for each project. The desktop version lets you set a per-project schedule for review. Just click the review button & the due date for review of all your projects is to be seen. Select a project, review it & click Mark reviewed & it moves back down to the next review interval.

Perspectives: Technically iPhone app supports these now, but they have to be created on the desktop. For example, I have some tasks that have to be done on my home computer, others that have to be done at home. Theses are 2 different contexts. I also can check email, online & general Mac contexts at home. With perspectives, I can group all those contexts into my "Home" perspective. My work perspective includes general Mac, online, email & any office-only contexts.