In feedback I get, people hve most problems getting glass to lay nicely around stems with no air entrapment and avoiding puckering at the center of the kayak along the shear. Also in the size and commitment of the mixing and applying of large amounts of epoxy. Since the deck on most kayaks is so flat, the coating of glass is usually a no-brainer and less intimidating than doing an entire hull for the first glassing project.
When most people have the choice, they usually go for the deck first for the mentioned reasons and actually almost all of them come out perfect.
However, it's up to the builder! I recommend the deck in my manual for the first glassing job.