Without them, does everyone just research everything?
More likely everyone still only researches the Melee/Metal line or Adepts.
1. Removing Flurry
Recall the huge discussions about how 'useless' the Horse and Boat unit lines are, and you'll see that the exact same issues apply to the Archer line. At least the Crossbow line contains useful techs (engineering, machines). Now I'm not saying that adding the Flurry back in is what's needed, but honestly even the Elves + 1 STR doesn't make Archery units that much more attractive over Melee or Recon lines and they still have Flurries.
2. Patriarch
I really liked this as an 'flavor of the world' idea, but found the implementation to be a complication. My main problem with the previous mechanic was it wasn't obvious when you could 'Patriarch' a unit, and the need for the user to cast the spell made it confusing to newer users. The 'Call Holy War' spell made even more confusion, and that can gladly go.
I'd encourage you to consider keeping the promotion and moving the mechanic to a Global Event.
Gaining the Patriarch promotion grants +1 (typed) STR (Type depends on religion?), and the Free Promotion promotion.
Event: Ascension by Acclaim
Timing: Common, Triggered separately for each religion.
Requirements: [Religion] must at least X% spread across the Civs.
Triggering [Civ] must have a High Priest of [Religion] unit of at least level 6.
No other High Priest of [Religion] with the Patriarch promotion can exist
Text: "Popular acclaim demands that the High Priest of [Civ] be recognized as the Patriarch of [Religion]. The other people's of the world will be watching your actions closely."
Choices:
1. "Use [Civ's] influence to secure the Patriarch (Costs [Max(5% Treasury, 100)] gold)"
Result: -X gold, Priest gain Patriarch Promotion. -2 Diplomacy with all other Civs for 20 turns, +1 Happy for 5 turns.
Global Text: "At [Leader's Name] urging a new Patriarch of [Religion] has been named in [Civ]."
2. "Leave religious affairs to the pious"
Result: 50% chance of Patriarch promotion, +25% if you also have the holy city.
Global Text: "The people of the world rejoice as the Patriarch of [Religion] has been discovered in [Civ]" or no message if promotion was not granted
3. "Such a religious figure would upset the balance of power"
Result: No Patriarch promotion, +2 Diplomacy with all other Civs for 20 turns.
Global Text: "You can thank [Leader] of [Civ] for insuring that no Patriarch of [Religion] will interfere in world affairs"
Further Events to remove the promotion or shift it between Civ's follow naturally.
3. Golems
I'm not at home to check, and the wiki is down, but isn't the Nullstone Golem the Shield Wall UU? I remember liking the Arcane Golem, but now I'm confused. I would be concerned with how many National t4 units the lurchip have access to compared to the other civs (The other Civ's kept the UU's even if the UnitClass was removed).
Also, why lose the Copper Golem (Maceman UU) but keep the less useful Gargoyle UU (pikeman UU)? Seem's like a conspiracy in Golem town.
The Golem customization building were a neat flavor, and I'd love to see that flavor retained in some simpler way. Since I'd assume the Wood Golem now requires either Forges or Training Yards (previously Golem Workshop), a Unique build on that Building class would be nice, perhaps a targetted global spell (al la Secrets of Sarona) to grant all Golems in the stack a customization promotion?
Obviously, I'm guessing at what the additions but I think that Flavor should be preserved even if the mechanic changes.
Love
Vilnon