People often complain of how religious and mystical they make the non-European civs, but there is also the problem of how irreligious the western civs are portrayed. In the era of the Reformation and Counter-Reformation, religion was hugely important in the west and some European holy sites could help remedy the lack of focus on it.
Hospitaller Commandery
This is more of a thought experiment to show that essentially every important element of the Malta civilization can be fully (and arguably better) represented in a minor civilization. Unfortunately, we got a full civilization based on an insignificant island that plays like a crappy mod full of made up units and recycled content.
A Hospitaller Commandery holy site would be applicable to essentially every European map, and even the Caribbean if you take into account the Hospitaller colonies. Although they were originally a Catholic military order, Protestant offshoots broke off during the Reformation and the Order had a strong presence in Orthodox lands and relocated to Russia after Napoleon captured Malta.
Units
Hospitaller Knight - Strong swordsman with the deflection ability. More or less the same as the current Maltese unit.
Fixed Gun - Instead of being a weird unit-building hybrid, Fixed Guns could feature just like they are in the campaigns, and be an indestructible structure built into the holy site. Researching a technology would enable taking control of the gun. Control of the Fixed Gun would be determined by whoever has control of the holy site, so destroying the Trade Post would disable it.
Order Galley - Galley with promotions and a bonus against mercenary warships. The mission of the Knights became to defend Christian shipping against Barbary pirates so a bonus against mercenary warships is fitting, and gives a counter to the Battleship enabled by royal houses.
Technologies
Powder Magazine - Enables Fixed Gun and detonation of Trade Posts
Crusader Knights - Hospitaller Knights gain bonus attack near buildings
Holy Infirmary - Allows Hospitaller Knights to build Field Hospitals
Papal Basilica
Instead of only being confined to an element of the Italian civ, a Papal Basilica could represent the influence of the Roman Catholic Church across Europe. Even if this were added, Italians wouldn’t necessarily need to lose their Papal units, they could just use the holy site ones instead of them being weird pseudo-mercenaries. It could feature on most southern, western, and central European maps.
Units
The units of the Papal Basilica would be the most iconic of the Papal armies. They would exclude “Papal Lancers” since these were essentially the exact same thing as Elmetti, and “Papal Bombards” because those are just made up.
Papal Zouave - More or less the same as the current Basilica unit.
Swiss Guard - More or less the same as the current Basilica unit, but renamed from Papal Guard.
Order Galley - The Papal States participated in major sea battles like Lepanto and supported the Hospitaller efforts of countering Muslim piracy, so they could also enable Order Galleys.
Technologies
Indulgences - Gain coin for each unit lost
Papal Interdict - Increases the experience cost to your opponent’s next shipment
Concordat - Receive the benefit of your last age up bonus again (similar to the Advanced Politicians card)