The Player's Handbook says that a cleric prepares one or the other of the two domain spells available to the character at each level each day. This implies that the cleric cannot prepare a lower-level domain spell in a higher-level slot. It also implies that a cleric cannot use metamagic feats on a domain spell since that would require a higher-level slot. Wizards who have specialized in a school of magic would seem to face a similar restriction. Is this what was intended?
No, that's not what was intended, though the wording of the rules certainly implies that is the case. Each domain slot can hold a spell only from one of the cleric's domains, but a cleric can use metamagic on domain spells (which makes them fill up higher-level slots), or the cleric can simply prepare a domain spell in a higher-level domain slot.
