Since KoL is busy with work today and Windel has spotty internet, I'll answer.

[quote=@BCTheEntity]

1. How does the Heaven > Machina > Hell > Heaven circle work? Is it only specifically each race's supernatural powers and gear that are affected, or would any sufficiently-aligned physical substance also be affected by that? Are there any other concepts that those conditions might apply to?
[/quote]

The Faction effectiveness dichotomy has never been something as severe as something as the type match ups of Pokemon or any other RPGs, but more of an edge to compile upon those you already posses. The Holy powers of most angels is effective against demons, obviously. Demons naturally warp the world around them with their corruptive influence, which is remarkably effective against the Machina if anyone can understand how catastrophic change a 1 to a 0 can be in even basic coding. Machina's advantage is in some regards the weakest, as it comes from resistance rather then increased lethality, against the angelic powers. An exorcism on an uppity coffee maker won't stop it from short changing you in the morning. 

As for how this plays out in practice? That's a matter of how invested you are in utilizing tools attuned to the faction's specialty. A Machina picking up an advanced railgun is going to do well ignoring a barrier of magic, though if an Angel picks one up and shoots a demon it won't have the same value unless they go through some effort to consecrate the thing. 

[quote]2. What distinguishes each faction's land holdings from the rest of the Nexus? Does each faction have their own pocket dimension containing their capital city/headquarters? I'd assume they aren't all in the same dimension, but is there some factor that determines how many jumps a given entity has to make to move from a particular faction's dimension to another, or could a being theoretically dimension-hop straight to Hell from Heaven, or perform other similar factional crossings?[/quote]

If you ever heard of Planetside 2, then you can grasp the state of the Factions' capitals. They all exist in the same dimension and are in far off corners. They field vast armies battling along shifting borders, with the RP focusing on the more exceptional combatants in their own events. Now this means that they physically exist and can thus be entered, but what everyone seems to forget is that the capital of a militarized nation existing for the purpose of being militarized has fantastic security. Hell is self explanatory. The Machina are more obvious. And Heaven...well, you don't need to be a theoligist to understand how all the glitters are not gold.

And there are the clearly biased Vassals who don't want someone to launch a nuke from Hyperion to Celestia, or the Angels to summon an eldritch horror of the divine and smite the underworld. So causing a ruckus is bound to make Iona, Hoho, Juno, or the Eel come down upon them.

[quote]3. What's the idea behind the Eyes? Do they denote some particular destiny - are their bearers likely to have some special role to play when the Great Danger finally rolls around, or do they just act as a generic high-tier powerup that improves their chances against the Great Danger and other foes? What routes can be taken for somebody to get them within the game, assuming they're in a special role and so able to acquire them? Is it just "unlocking your potential", or are there other means of getting them?[/quote]

The eyes are simple. Within the Nexus, they are a great power bestowed by the leaders or powers beyond them as a boon for exemplary service to their faction. They don't denote your destiny and they can be taken away, so it's just a high tier power up. Considering the Vassals are refraining from being active participants it would be hard to say where you could get them outside of the three leaders.

[quote]4. And what's up with the Great Danger, anyway? It seems like the scope of the game doesn't quite cover how that's going to work out at this stage, when it ultimately represents what I assume is the game's final boss. Will there be warning signs that it's beginning to come close to the Nexus? Will we receive preparation time to try and handle it? What sort of powers are we expected to wield in order to stand a chance against it?[/quote]

That's hard to discuss, in no small part to plans getting FUBARed along the way. I can't say more beyond the fate of the Happy Verse and whether that happens or not is tied to it.