Shared merits and lairs are the same thing. Factions are groups of people sharing something, be it a merit or a template. Finding people who share a template is sometimes called a "census".
An automated/calculated group is a census. A manual group is a faction. Adding them both together, I will call them factions.
Changeling pledges and Demon contracts are factions with a limited time span and/or their own stats. That is, they are Factions + Character Sheets.
A lair is a faction with a character sheet.
If we store these "sheets" as notes, we can use the same base code to deal with all of these things, with a tag whether or not we're talking about lairs, contracts, locations, or who has Strength at 3+.
This is not dissimilar to notes, views, and backgrounds, but an order of magnitude more complex. Maybe two orders.
Edit: The Aether Faction code already stores notes about factions, it is simply not powerful enough to handle the added complexity of the diversification involved. The way we used it on Reach, it was far past due. Imagine have a High Society faction with people of Socialize 3+ always on, but being able to add others as needed. Imagine having a +faction vampire that was always up to date, no matter what. Imagine being able to put someone on a faction via a time limit and you have Pledges. They all share a foundation.