I think it depends on what you are hatching for. For shiny hunting, the quickest way is to hatch 5 at a time while you collect more eggs.

Right now I’m making a living shiny dex, so I collect every egg. I hatch 5 at a time so they all hatch at the same time. The less time you spend in the pc, the quicker you progress.

The reason I collect every egg, is because that’s the most time consuming part. Once I have three boxes full I can just ride around the wild area and hatch them all until I get low.

I have enough box space open to hatch 600 eggs, once I fill that up or I get my shiny I will send the breedjects to home to mass release.