What I've got in mind so far. Sound off in the comments, most especially civic changes and condensed thoughts from finished games? Also wanting thoughts on what to do with the Wither Promotion, Spirit III, and Shadow III.
EDIT: Pulled in the comments from the first several posts (Bob, Mardoc, Selrahc) Changes from the original are in green.
EDIT: Pulled in more suggestions. Changes from the original are in cyan.
EDIT: Pulled in bugs mentioned elsewhere and universal CIV BTS bugs. Changes from the original are in red.
EDIT: If the item is struck, it means I've added it to the latest build I have. If it's bolded then I've also tested it. When everything is struck and bolded, we get another build!
Balance:
Structural:
EDIT: Pulled in the comments from the first several posts (Bob, Mardoc, Selrahc) Changes from the original are in green.
EDIT: Pulled in more suggestions. Changes from the original are in cyan.
EDIT: Pulled in bugs mentioned elsewhere and universal CIV BTS bugs. Changes from the original are in red.
EDIT: If the item is struck, it means I've added it to the latest build I have. If it's bolded then I've also tested it. When everything is struck and bolded, we get another build!

Balance:
- [STRIKE]Sidar Wanes @ Lv. 6[/STRIKE]
- [STRIKE]Tsunami Fix (Range 1)[/STRIKE]
- [STRIKE]New Promo: Favored (as Arcane Potency, but only for Disciples).[/STRIKE]
- [STRIKE]Spiritual grants favored and Mob1 (Disciples)[/STRIKE]
- [STRIKE]Arcane grants potency and Mob1 (Arcane)[/STRIKE]
- [STRIKE]Falamar loses Adaptive[/STRIKE]
- [STRIKE]Ljosalfar can build Alchemy Labs[/STRIKE]
- [STRIKE]Svartalfar can build Alchemy Labs[/STRIKE]
- [STRIKE] Conquest reduced to +2XP from +3XP[/STRIKE]
- [STRIKE]Command Post reduced to +2XP from +3XP[/STRIKE]
- Council of Esus Changes (See Post Below)
- [STRIKE] Spirit III Spell gives +50% GPP and cures Enraged[/STRIKE]
- [STRIKE] Shadow III Spell summons a Mistform w/ Marksmen[/STRIKE]
- [STRIKE] Wither Promotion gives -1 Defense along with its other penalties[/STRIKE]
- [STRIKE] Sons of Asena costed the same as standard Axemen[/STRIKE]
- [STRIKE] Javelins somewhat cheaper (30H, quick speed)[/STRIKE]
- [STRIKE] Diseased Corpses do not go Obsolete[/STRIKE]
- [STRIKE] Give Specters Death Affinity, remove fear, str. 3[/STRIKE]
- [STRIKE] Boar Riders (Khazad Horsemen) get +40% v. Mounted[/STRIKE]
- [STRIKE] Horse Archer hammer cost restored to original[/STRIKE]
- [STRIKE] Arturus Thorne set to IND/ORG/ING from FIN/ORG/ING[/STRIKE]
- [STRIKE] Fix Consumption Popup[/STRIKE]
- [STRIKE] Fix Basium to properly apply immortal only some of the time[/STRIKE]
- [STRIKE] Fix 7 Pines (Likely Python Broken)[/STRIKE] WAD
- [STRIKE]Change Arcane Lacuna to not require any improved nodes (+0 XP but still block casting)[/STRIKE]
Structural:
- [STRIKE] Adaptive does not remove earned traits[/STRIKE] Only works for case: (Illian Aggressive). Where else can you earn traits that might be removed by Adaptive?
- [STRIKE] Insane does not clear Civilization traits (Perpentachian Kuriotates)[/STRIKE]
- [STRIKE] Change Cassiel's religion weightings so he can adopt a religion if not agnostic.[/STRIKE]
- [STRIKE] Sheelba loses BAR[/STRIKE]
- [STRIKE] Jonas loses BAR[/STRIKE]
- [STRIKE] Clan of Embers gains BAR as CivTrait[/STRIKE]
- [STRIKE] Game Option for Basium to spawn as a human player (Off by default)[/STRIKE]
- [STRIKE] Game Option for Hyborem to spawn as a human player (Off by default)[/STRIKE]
- Tholal's v1.8 or 1.9 if I can find it. He's up to 2.1 right now but it adds some functionality which I don't want to worry about (revolutions, puppet states, BUG, etc.)
- [STRIKE] Traderoute Bug Fix[/STRIKE]
- Production Automation Bug Fix
- Build Culture Bug Fix
- Multiple Techs from Oracle/Tower of Divination Bug Fix
- Reach for the City Capture Culture Conundrum Let's hold off on this one for now.