Well I decided to post this after reflecting on the utter lack of Unitology presence in Dead Space 2. It was like 90% EarthGov, 10% Unitology; and I'm not saying that's a bad thing, and it even makes sense in a story-telling format.
The primary "villains" in each respective game obviously determine the focus:
Dead Space: Challus Mercer - fanatical Unitologist. The Unitology focus is supplemented by a large amount of logs fleshing out the nature of the religion, and leaves it hanging with the enigmatic Mausoleum Ships. Extraction ties in with the first game, and establishes even more of a Unitology presence by revealing Lexine's role and establishing that a vast majority of the Ishimura's crew was replaced with complementary Unitologists prior to the mission to Aegis VII. Obviously CEC is headed by Unitologist interests.
Dead Space 2: Hans Tiedemann - Morally conflicted government strong-man. The last point through my first playthrough that I thought "Seems like a lot of Unitology stuff is going to be revealed in this game" was a second before the EarthGov gunship drops in and chops up Daina Le Guin. Then, and quite literally, Isaac falls (get it - because of the vent shaft :P) progressively further into EarthGov focus and territory. I thought this was an amazing approach by the writers and thought they pulled it off perfectly.
Anyway, by focusing almost entirely on EarthGov, in DS2, we get almost equal balance between the two forces, Unitology and EarthGov. And we've got mysterious parties on both ends: Tiedmanne's Overseer, and Warren Eckhart's mysterious Unitologist superior whom he calls "Enigma Lange"
So I really think these two forces are going to erupt and clash in conflict in Dead Space 3, revealing tons of elusive sh** that we all want to know about, and really just being amazing.