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Unfortunately, putting the due date on the final step is equally misleading, since then it's only that step that shows up as "Due" which is going to be completely out of order. The way I've worked around it for now is to create a separate task in a Misc-actions bucket and put the due date on that task, leaving the actual project with no due date.

Really, it's not even so much the counter that's the issue -- I'd probably have less of a problem with the due count being so high if the "Due Soon" and "Overdue" categories at least had a hierarchy to them (ie, list the projects and then the tasks within those projects). The way it is right now those categories are virtually useless, as they simply list a whole slew of unrelated tasks in no discernible order. If there was a hierarchy, then at least I could clearly see which projects were due at a high level, rather than seeing 80 individual tasks scattered about.

Personally, I'd suggest that if the project has a due date but none of the individual tasks have been assigned a due date, then the due count should reflect that single item -- the project as a whole. If the individual items have a due date, then by all means show them up individually, since each one may be different in that regard.

That approach would take care of the scenario you describe where a prerequisite task has no due date yet a dependent task does. Personally, however, I'd suggest that OmniFocus simply shouldn't allow this to happen at all.... If you have a sequential project, prerequisite tasks definitely should inherit the due dates from later dependent tasks, in much the same way a due date for an entire project is inherited by all of the tasks contained within that project. Right now there are a number of other areas within OmniFocus, both on the desktop and the iPhone, where that scenario would end up being confusing at best (a due count showing up on a context with no due tasks visible), or biting you badly at worst (the due task being missed entirely as the dependent task had not yet been completed).

IMHO, the best solution would likely just be a third configuration option in the Settings on the iPhone similar to the options for Project and Context view.... A "Main View" setting that allows the user to choose whether Due-Soon/Overdue/Flagged categories show Next Actions, Remaining or Available. Then, further to this, ensure that the counts are consistent with the option that has been selected. As I've already noted, this is a problem that is apparent in Context view... Showing a Due-Soon/Overdue count for tasks that are otherwise invisible to the user, exacerbated by the fact that there's no simple way for the user to change the filter to display these tasks, and no notification that they would even need to do this.