Focused Domain: A theologian chooses only one domain from her deity's portfolio rather than the normal two domains. All level-dependent effects of the granted powers from the theologian's domain function as if she were two cleric levels higher than her actual cleric level. This does not allow her to gain domain-granted powers earlier than normal.
A theologian can prepare domain spells using her non-domain slots. She cannot use her spontaneous casting ability on domain spells, even if they are prepared in non-domain slots. In all other respects, this works like and replaces the standard cleric domain ability.
Domain Secret (Ex): At 5th level, the theologian chooses one domain spell. That spell becomes permanently modified with one of the following metamagic feats: Bouncing Spell, Disruptive Spell, Ectoplasmic Spell, Enlarge Spell, Extend Spell, Focused Spell, Intensified Spell, Silent Spell, Still Spell. This metamagic feat does not increase the level of the spell. Once chosen, this modification cannot be changed. The domain specialist need not have the metamagic feat to apply it to a spell using this ability. At every 5 levels after 5th, the domain specialist may choose an additional domain spell to modify in this way. She cannot modify the same spell more than once.
Diminished Spellcasting: A crusader chooses only one domain and gains one fewer spell of each level than normal. If this reduces the number to 0, she may cast spells of that level only if they are domain spells or if her Wisdom allows bonus spells of that level.
Bonus Feat: A crusader gains a bonus feat at 1st level, then again at 5th level and every five levels thereafter (to a maximum of six at 20th level). These bonus feats must be chosen from the following list: Heavy Armor Proficiency, Improved Shield Bash, Martial Weapon Proficiency, Saving Shield, Shield Focus, Tower Shield Proficiency, and Weapon Focus*. At 10th level, a crusader may also choose from the following feats: Exotic Weapon Proficiency, Greater Shield Focus, Greater Weapon Focus*, Improved Critical*, Shield Slam, Shield Specialization, and Weapon Specialization*. At 20th level, a crusader may also choose from the following feats: Greater Shield Specialization and Greater Weapon Specialization*. Bonus feats marked with an asterisk (*) must be applied to the favored weapon of the crusader's deity. A crusader need not meet the normal class- or level-based prerequisites for these bonus feats.
Legion's Blessing (Su): At 8th level, a crusader gains the ability to confer beneficial spells quickly to a large group of allies. As a full-round action, the crusader may confer the effects of a single harmless spell with a range of touch to a number of creatures equal to half her cleric level. The spell's range remains touch, so all intended recipients must be within the crusader's reach when the spell is cast. Using the legion's blessing expends the prepared spell, but it also requires the crusader to sacrifice another prepared spell three levels higher, as when spontaneously using a cure or inflict spell. The higher-level spell is not cast but is simply lost, its magical energy used to power the legion's blessing.
The reason I ask is because Focused Domain and Diminished Spellcasting do almost the same thing but are not replacing any of the same abilities.
I'd say they both alter your domain selections, so no, they don't stack.
One replaces the Domain feature (Theologian) and the other one alters it (Diminished Spellcasting alters your Domain feature to only getting a single domain). So, no, they cannot stack.
And it does not matter that Diminished Spellcasting does not specifically call out the Domain feature, it still alters it.
And it does not matter that Diminished Spellcasting does not specifically call out the Domain feature, it still alters it.
I would say though that because they don't specifically call it out that it should be allowed. Yes,they are both technically altering the domain ability, however both are being altered in such a similar way that it seems as though it would work together just fine. Both archetypes state that you can have just 1 domain, why cant they both be the same domain?
Both archetypes state that you can have just 1 domain, why cant they both be the same domain?
For the same reason that I can't pay for a $2 item using the same $1 bill two times. IMO, of course. If you're the GM, you're free to allow it.
Yes,they are both technically altering the domain ability
This is all you should need for your question to be answered.
As you quoted:
"...none of the alternate class features can replace or alter the same class feature from the core class..."
That's the end of it. The rules are crystal clear.
however both are being altered in such a similar way that it seems as though it would work together just fine. Both archetypes state that you can have just 1 domain, why cant they both be the same domain?
Well, because of the rules. Here's the thing--you can make that argument and either create a houserule (if you're the GM) or convince the GM to houserule it. However, it will be a house rule, because the actual rules are very clear about the issue.