"John the Revelator"Thraben Doomsayer/False Prophet/Serra Ascendant: Doomsayer is "terribly inefficient." Thematically speaking, False Prophet would make for a great addition. However, I'd like to get the most out of Avacyn, Angel of Hope whenever she's on the battlefield and exiling all creatures in play doesn't quite accomplish that. Without True Conviction or Baneslayer, I'd have to draw Serra Ascendant early on for the bonus. Replaced with Mad Prophet as "John the Revelator".
The Son of ManGideon Jura/Reveillark: Gideon's "not terribly efficient" in the deck and Reveillark isn't useful with the deck's creatures. Replaced with Sun Titan.
The Heavenly Host/"Onward Christian Soldiers"Luminarch Ascension/Entreat the Angels: I'd rather pay 8 and definitely get two angels (barring countermagic, of course) rather than hope my enchantment doesn't get blown up going around the table. I run Decree of Justice over Entreat the Angels since it not only provides more options, but potentially more bodies. If I only have 6 mana, Entreat will only get me a 4/4 while Decree gets you three 1/1s and a card.
The Four Horsemen of the ApocalypseStoneforge Mystic: More fragile than Stonehewer Giant and less useful in this deck. "Conquest", the 1st Horseman of the Apocalypse slot, is currently filled by Stonehewer Giant.
Gratuitous Violence/Avatar of Slaughter: It's not likely the deck will have a horde of creatures in play. All the more reason to run a creature over an enchantment, I think, especially since about half the deck's creatures are for utility anyway. However, the Avatar is dangerous without Gisela on the field. "War", the 2nd Horseman of the Apocalypse slot, is currently filled by Nobilis of War.
Mageta the Lion/Scourge of Kher Ridges: Mageta requires too much discard. Replaced with Jaya, which Sun Titan recurs. Jaya comes down several turns before the Scourge of Kher Ridges and, in a deck with only 36 lands, I can activate her ability before I can reliably cast the Scourge. To top it off, she hits all creatures, flying or otherwise. Finally, for flavor reasons, the deck only runs one dragon, Knollspine. "Death", the 4th Horseman of the Apocalypse slot, is currently filled by Jaya Ballard.
7 ArchangelsReya/Iona/Radiant/red Akroma/Basandra/Razia/Indomitable/Platinum: Reya and Iona cost too much mana; the deck doesn't run enough creatures to pump Radiant; one Akroma is enough, thank you; I happen to like combat tricks; Razia is too expensive for what she does; not enough artifacts; irrelevant without Indomitable. The deck's seven archangels were chosen based on a need for diverse mana costs, flavor, and synergy with Gisela's abilities.
7 SealsRout/Day of Judgment/Terminus/Hallowed Burial/Catastrophe/Austere Command/Bonfire of the Damned/Akroma's Vengeance/Obliterate/Devastation/Chain Reaction/Blasphemous Act: Wrath of God stays in. It's the cheapest board sweep the deck has and I can cast it without ramping before turn seven relatively easily, unlike Rout. DoJ is "strictly worse" than WoG. Terminus/Hallowed Burial, Catastrophe, and Austere Command don't interact as well with Gisela like Fault Line and Earthquake do. Inferno affects more of the board than Bonfire. I'm running enough artifacts to not want to bother with Vengeance or Obliterate. Difficult to abuse Devastation without Avacyn in play and no synergy with Gisela. Chain Reaction/Blasphemous Act are both too conditional and neither fit the deck's theme.
DoJ==>Rout==>Razia's Purification
Terminus/Hallowed Burial==>Catastrophe==>Fault Line
Austere Command==>Earthquake
Bonfire of the Damned==>Inferno
Brightflame/Pyrohemia: I tended to opt for cards that didn't depend on having Gisela in play to maximize their usefulness.
7 TrumpetsThunderous Wrath: "Inefficient." Dropped for Angel's Trumpet for obvious flavorful reasons.
Oblation: Dropped for Swords to Plowshares. Banishing Stroke seems like a better choice, regardless.
Cessation/Faith's Fetters/O-Ring: Dropped for Prison Term, which is both flavorful and effective.
Evangelize/Heat Shimmer: The first one is "heavily costed in colors that can't ramp well, and is super color intensive. Sorcery speed as well." Shimmer doesn't fit deck's theme. Replaced with Word of Seizing.
Flaming Swords & Angelic RaimentsChampion's Helm: Mask of Avacyn works with the deck's non-legendary creatures.
Moonsilver Spear: High equip cost.
Skullclamp: Not useful in this deck. Running Mind's Eye instead.
Sword/Shield of Kaldra: Not recursible with Sun Titan.
Sword of Feast and Famine: Doesn't combo with Gisela's abilities like F&I and W&P.
The ResurrectionDefy Death/Miraculous Recovery/Karmic Guide: Resurrection is more flavorful. Also, the FNM art is amazeballs!
Armageddon, the Last BattleAggravated Assault/Insurrection/Waves of Aggression: It only costs five mana to get a total of four combat phases out of World at War, and its castable well before Insurrection. It's difficult for the deck to cast Assault and activate it the same turn. "Armageddon", the final battle slot, is currently filled by World at War.
Holy RelicsArmillary Sphere: Dropped for Scroll Rack/Land Tax combo.
Darksteel Ingot: Dropped for Mana Vault.
Streets Paved With GoldRupture Spire: "Downright awful."
MiscellaneousValor: Trumped by Glory and usually unnecessary with Gisela.
Preacher: Too campy.
Brilliant Halo/Runed Halo: Brilliant was for flavor only and pales next to the deck's equipment, whereas Runed is too narrow.
Darksteel Forge: Dropped along with Platinum Angel.
Sensei's Divining Top: I think the deck benefits more from card draw. Plus, I'm still running Scroll Rack to help out with top deck manipulation.