I think the Devs at one point said on "evil playthroughs" (presumably alliance with the cult of the absolute, but I suppose it could also be allying with Raphael or something - I suspect the actual branch is at Moonrise Towers) there would be characters who were major allies who you would never meet on a "good playthrough". Also the way they talk about having to "commit" to specific companions at some point suggests a fairly serious branch there.
