Cranidos, Rampardos, Shieldon, and Bastiodon are not included in this egg group either. This is because they represented terrestrial extinct animals, as Archen and Archeops does. (and now a days with the inclusion of Tyrunt and Amaura, it reduces this pattern even further).
Cranidos, Armaldo, Kabutops, Omanyte, etc were fossils, yes, but they all represented extinct, aquatic invertebrates. So, it was appropriate for them to be in water 3. It doesn't make sense for Archen and Archeops to be in there. So it is still a mystery as to why this was done.