I won't go in depth but here's a small list of things I expect in some shape or form:

With us now more aware of the need for balance, there will be a few grey areas:

-- Elidibus in some form meeting Minfilia - the two Emissaries.
-- Elidibus being less inclined to have us killed now that we're WoD's.
-- Elidibus having to content with Resonant Zenos (attacked, mayhap even killed).
-- Gaius Van Shadowhunter happily slaying Ascians is likely not a good plan for a consistent/balanced future if it tips the scales too far in favour of Hyde.
-- Whatever we do in ShB/1st will buy enough time for Black Rose shenanigans on the source and cause a renewed need to focus on the empire on our return.
-- A conflict between Varis and Solus, given the blatantly obvious hints that while Varis is going along with his alliance with the Ascians, he is not in the slightest bit happy with the fact they are pulling the empire strings. This will likely have something to do sabotaging the clones.
-- While I have no doubt Varis is wholly behind mankind over the Ascians, I'm not entirely sold on him being fully behind the plan of an outright rejoining. Particularly in the "Black Rose" cutscene, it gives you the impression that Varis is just playing the part of puppet to placate Solus, but is otherwise not happy.
-- Resonant Zenos as a whole. The predictable idea (see Pt.3) would be for him to attack Elidibus, likely after we come to fully understand Elidibus (as emissary) has just been doing what he deemed necessary in the name of balance (ie. not exactly Evil McEvil). Cue Resonant Zenos wanting his body back and causing trouble at the worst possible time. As such, with a dead emissary and an ascian slayer on the source unchecked, even if we help to bring back some darkness to the 1st, there's a whole lot of Hyde-balance issues that may cause us problems on the source.

Regardless, I fully expect this expansion to pull at the morality string from time to time. It's one thing just slaying red-shirt beings of 'light' that are made to seem conveniently 'bad' to not make us feel awkward, but to actually have the WoL make some less than noble decisions? Now would be the time to throw mud into the water and really test how far we'd go in the name of Darkness, without losing ourselves.