-CCYB: No debate. Even without Antimatters, this deck crashes and burns against Permafrost Shield + tons of SoG/Sanctuary, and the deck can't do much against a quinted Lava Destroyer, FFQ, or (especially) Blue Nymph.
-RoL/Hope: Also good counter, like against Divine Glory. Not helped by the fact that Archangels and Light Dragons are really, really hard to kill for this deck.
-Timebows: Could you give me a sample deck? I know they exist, but I haven't actually seen one.
-Maximum damage per turn of IGT: 8 GotP * 9 damage per GotP + 3 Eternity * 4 damage per turn = 84 damage per turn. Cue Miracle. This deck has a wait-time of 4 turns in between Miracles, so it needs at least 337 max HP, or 6 SoD. That's not happening, so Pendulums would indeed help. Of course, this assumes the FG won't Thunderbolt the fractaled Ghosts into oblivion, and the IGT player fractals with nothing in hand. If it kills just three GotP (very feasible, given it has nothing else on which to use all those Thunderbolts it draws and saves up), it only needs to meet the much more manageable goal of 2 SoD to be able to chain Miracles. There's nothing for IGT to draw-lock this FG with, either.
Of your concern for bursting out a Fractal after gradually taking the FG's HP down to 84 HP: Assume the rather artificial scenario that three Eternities are laid down on the first turn (this is the maximum amount of damage possible before the Fractal). You need 10 turns to take the FG down to Fractal burst range, which is quite achievable. However, each SoD will add two turns to that counter. At 4 SoD, you need 18 turns to take the opponent down to Fractal range- but, unfortunately, that also happens to be the exact number of turns you can stall with Phase Shield.