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One consideration is that A allows you to use all of the OmniFocus tools for managing each big chunk of work separately, whereas B does not. You can't review individual sub-projects (aka action groups), you can't put them on hold or drop them, and you can't filter them from view in the way you could if you made each independent unit a project. Of course, if you've already published a syllabus saying that you're doing XYZ week 13, maybe that flexibility isn't available to you.

OmniFocus also does a bit of implicit prioritization by the ordering of material in the sidebar. Might be easier to take advantage of that with individual projects rather than rearranging the innards of a big project. If you got in a jam, you could pull out the projects for various parts of your courses to put them up at the top, which you couldn't do if you've gone with action groups.

What are you teaching? I want to have suitable examples if I need to illustrate something no point in referring to chapters in an art history book if you're teaching VLSI design :-)