[RPG] What happens to the domain slot if I trade all the domains for domain feats

The Good domain allows you to cast spells with a +1 caster level. While by itself, the power is hardly impressive, it has excellent synergy with the Aligned Spellcaster ACF (DR357). You sacrifice gaining a familiar to add the [Good] descriptor to all of your spells (in addition to a further CL bonus vs evil aligned/subtype creatures). This means that every spell you cast (maybe not evil spells) gains the +1CL from the Good domain power. There are metamagic feats that can also add the [Good] descriptor to spells, but I find this method to be less effective. For further [Good] descriptor synergy, throw in Spell Focus(Good) (BoED) to gain +2 DC on all spells with the [Good] descriptor. Yes, it's more powerful than Spell Focus(School) and applies to every spell you cast. Maybe a little cheesy, but balance is always a delicate thing in 3.5.

The word include indicates a subset: every element that is included appears in the including set.

So the statement about the cloistered cleric’s class skills is that the given list, “Decipher Script, Speak Language, and all Knowledge skills (from the Knowledge domain, see below),” is a subset of the full set cloistered cleric class skills. This explicitly does not tell us whether or not this is the complete list: the word includes means that these skills definitely are present, but does not say whether or not anything else is also present.

However, the statement that the class operates as normal for that class unless otherwise specified does tell us about the complete skill set: it also includes the original cleric skill list.

So the complete list must include both the original cleric skill list, as well as the specifically named skills. They are, in effect, added. Which is consistent with the description of how skills may be changed: variants may list “Additions or subtractions from the class skill list,” but the rules do not allow for the possibility of outright replacement. Only additions and subtractions are allowed. Since nothing in the cloistered cleric description explicitly subtracts any of the original cleric class skills, the cloistered cleric has each as a class skill.

Would it have been clearer if they’d just said “add”? Yes. I don’t know why they didn’t. But despite the lack of clarity here, the rules still amount to the same thing.

TL;DR: Cloistered clerics have all the cleric class skills, plus a few more