One thing about the Church: One problem that I had with EotFS (and which I swear to God, actually worked in one of the demos I downloaded but not in the final release??) was that the factionalism within the Church never worked, because:
1. The game started with ALL priests and churches in the Orthodox sect. Hence, the potential for intra-Church politics never materialized unless you deliberately started making all your planets follow a different sect.
2. There was no game effect from having the Patriarchy controlled by a different sect.
Now, as I said, in one of the demos I downloaded before I bought the game, the Church actually was split up. Each house backed a different sect, so the balance of power could be tipped pretty easily, and the Church wound up functioning as a microcosm of the struggle between the five Noble Houses. And....IIRC, each sect had different preferences in what techs they would proscribe. Like, the Eskatonics were the most permissive, the Avestites the least permissive, the Incarnates tended to allow "conventional weapons" but not exotic stuff like Plague Artillery, and Sanctuary Aeon tended to proscribe weapons, but not non-weapon related technologies.
IIRC, the pairings were:
Li Halan = Orthodox
Hazat = Avestites
Decados = Eskatonics
Hawkwood = Sanctuary Aeon
al-Malik = Incarnates
I believe the Church would even "un-proscribe" techs sometimes after a change of control (for instance, an Avestite patriarch being replaced with an Eskatonic one might suddenly see a bunch of techs suddenly allowed again).
There was a ton of in-game strategy potential there, for instance even though the Decados were generally in poor relations with the Church anyways, it was in their interest to push for an Eskatonic Patriarch, because their resource base favored a tech tree heavy in bioengineering and a number of typically proscribed techs.