Should I use ISO or OGC?

Existing workflows designed around or which use the OGC encoding may want to continue to use that method. New workflows might consider using the ISO. The OGC encoding conforms to ISO 32000 PDF, but ISO is also specified by it as well, so if a fuller conformance to that specification is desired, then that is an obvious choice. There are no significant technical reasons to universally choose one over the other, and TerraGo software support both.