Game 2 Chapter 3 appears to be limiting our “time spent” to two primary Grand Shayard factions (assuming that the “game’s code” screenshot that I found on Discord is credible), and your first faction choice feels pretty obvious (in my opinion): “The drudges and day laborers who work the manufactories of the city, load/unload trade goods at the river and seafront, and engage in petty smuggling/crime to make ends meet.”
(And PS: if you slaughtered Horion and Linos, your MC will gain massive credibility/reputation boosts with the drudges/day laborers, since they absolutely despise the Leilatous.)
Anyways, with the first choice now (presumably) picked by you, that leaves the second allied faction choice up for debate.
Quick followup question: is your MC hostile towards all nobles, priests, and merchants (by principle/knee-jerk reaction), or might a handful of compromises/unexpected alliances be formed with certain subfactions (of those hated groups)?
The mainstream/law-abiding merchants’ guild probably hates your guts too much to (willingly) work with you, but perhaps the more unsavory merchants (who are deeply involved with organized crime) may see your MC as a potential partner (and source of opportunity/profit), especially IF your MC could plausibly help out those merchants replace the aristos as the new elites in the post-Hegemony chaos.
Alternatively, why not infiltrate Grand Shayard’s nobility as a freeborn tradeperson? (and then fraudulently position yourself as the “lost heir of the de Syrnons,” thus claiming both leadership of the Laconniers AND the Shayardene throne)
It’d be quite the delightful irony for blissfully ignorant Homelander aristos to bow down to your helot MC, right? 
Perhaps the Laconniers will be more useful to you as mouthpieces (rather than becoming your next pile of aristo casualties/corpses)?
And if you want to treat the Laconniers as genuine allies (rather than mere pawns), maybe you guys could disregard each other’s aristo/helot upbringings to bond together over a shared “hard nationalism” worldview (being mutually “angry about the watering down of true Shayardene identity by the invaders’ culture”).
As for the Xthonic priesthood, the wiki mentions that they have a “secret branch of heretics.” If you didn’t ravage the priesthood too badly in Game 1 (merely inconveniencing them instead of antagonizing them into becoming “implacable enemies”), AND you were able to bribe priests during Game 1 Ch 4, perhaps you might be able to co-opt the Game 2 heretics to promote your Skepticism movement?
But perhaps the most useful “second faction choice” for you (in my opinion) are “the foreigners in the Merchants’ Pale.”
You’ll definitely want to deepen ties with Jevahir, the Nyrish warrior/spy/diplomat (since the atheistic Neres (as a whole) will most likely be very supportive of your Skepticism-driven movement).
Likewise, it would be very helpful to cultivate a relationship with the Abhumans (M’kyar, Laj-jas), so that your Wisard MC can learn plenty of useful self-sacrifice Theurgy techniques. (while also learning certain Abhuman techniques that will let you create better/more efficient Plektoi ).
You’ll also meet Halassurq agents in the Merchants’ Pale, and my opinion on how you should handle interactions with them is a bit mixed. You and Halassur share a common goal of ravaging/pillaging Karagon (and because the Laconniers are also allied with Halassur, you could further bond with the Laconniers over that common connection/benefactor), but at the same time, Halassur’s interest in dominating/invading Erezza makes it a horrible partner to ally with (in Cerlota’s eyes).
So anyways, to simplify/summarize things, you can ally with either Cerlota/Erezza or Erjan/Halassur, but not both (in the grander scheme of things).
Does this overlap with your earlier-mentioned “Sauron-like” ambitions of building a new empire, or will your MC instead be content to consolidate power in a freed/independent/united Shayard?
And how far does your MC’s definition of “his people” extend? Does it only refer to his fellow Shayardene helots/patriots, or might he later expand his vision towards freeing all of the Hegemony’s helots?
If he doesn’t give a damn about non-Shayardenes, then perhaps your MC now has convenient targets to Harrow (after the Hegemony has fallen, and the time has come for nation-building/tearing).
I don’t quite yet have a definitive picture/grasp on how a neutral Homelander/Cosmo reputation will impact your rebellion (by late Game 4/early Game 5), but I can at least inform you that the Leaguer aristo faction (in Game 2 and beyond) “will tend to like neutrals and Cosmo-light more than strongly Cosmo MCs.”
And it’s not unprecedented to “initially emerge from strong nationalism, and then later transition your faction into a cosmopolitan empire”; perhaps your MC might end up following Napoleon’s footsteps!
And this attitude extends to his own Skeptical/atheistic group of supporters, correct?
(Or might he instead play favorites here, in order to amass enough power to decisively secure the elective emperorship of his envisioned koinon, or alternatively become the “Mao-inspired” chairman of the new empire?)
Alternatively, do you have plans to initially rise on the back of the atheistic movement, and then later phase out its power? (in the name of your envisioned religious freedom policy)
E.g. appear the reasonable party by offering your opponent a bargain (that you covertly know/expect will be rejected), and then vanquish your “barbaric aggressor” opponent in honorable/direct combat afterwards? (while brushing off your detractors with “Eh, at least I tried talking before shooting!”)
Or did you have cleverer, alternative methods in mind? (That I haven’t yet considered)
(My imagined random, “small talk” post-Storm dialogue from Teren)
Teren: (looking at the carnage with binoculars) Welp, there goes my favorite bistro/hotel; I guess you owe me one (for looking the other way)! So anyways, let’s talk business!