Dispense with the threat of ceremorphosis ealier in the game, or even deal with the Elder Brain at beginning or in the middle of Act III, the tadpole is a leash that keeps you and the party on the railroad that is the Emperor-Githyanki-Absolute plotline which is what I was least interested in by the time I got to the city (because I'm interested in the city). Now the clash of ideologies that the need for a cure suppressed suddenly comes to the fore, as Tav and his companions now have to deal with three or more factions vying for power over the city's new Absolute sized power vacuum.
Now all your choices and the directions you and your companions' characters developed in acts one and two, metriculate into how things will play out in the denouement. As opposed to really only coming into play in flavor dialogue if you've brought them along, and within their own companion quests.
