In regard to your first point, that That Which Sleeps allows for evil empires while Shadows does not, I hope to correct for this, and allow both.
Internal vs external actions
I believe there are two core ways of interacting with the political system (Shadows' core): From inside and from outside. I'd like, ideally, for both to be fully polished, and for the game to be playable with exclusively one or the other. Currently implemented is the 'classic' approach. You first act from inside a society, by managing political favour, evidence, suspicion and shadow. Eventually you win, and the evidence, suspicion and shadow mechanics become irrelevant for this society. Your fellow nobles are now mad, and so you no longer need to hide evidence from them (nor do you have anyone to give evidence to, as they are all at 100% themselves). At that point, your gaze turns outwards, and you begin to command your society to slowly expand into others. In order to do so, and in order to avoid a Last Alliance type scenario, you must use powers on societies without having an agent inside them.
Ideally, there would be a rather clear distinction between 'powers to use to help your enthralled on their political journey' and 'powers to use to destabilise other nations'. Finding dissidents and arming them to cause civil wars, getting hated rulers elected, causing potential allies to fear each other, distracting nations with your Unholy Flesh...
If a player then chose to only play the inside game, they should be able to kill off their enthralled, and start again in a new society, working their way up, while leaving the old society in a state of darkness. In this way, the player has chosen to only interact with half the mechanics: the powers from the inside. With future expansions, I'd like for the outside-interference powers to become sufficiently developed that they can stand alone, and a player could just start a small evil empire in the wastelands/frozen north/scorching south, and use their powers to cause enough civil wars and infighting that they can progressively invade the whole map. This mode would never have the player take an enthralled agent at all, and never vote once. In service of this planned flexibility, the map already deliberately leaves spaces for the player to work with. The cold and hot areas are empty, and the map generation will reserve locations for non-human societies if the climate map doesn't provide enough uninhabitable spaces.
Since both types of power are needed for the 'classic' game, it should be fairly easy to give a bit of a buff to the 'interact with a society from the outside' powers and package it up alongside an evil-empire type set of powers, where you can invest in expanding your forces and give them basic commands (as you already can with the Deep Ones).
Wedge Issues
As to your culture/religion/nationalism, I hope, possibly optimistically, to make the situation a bit more emergent and situational. I consider these as 'wedge issues', political points which you can bring up in order to divide voters and set them against each other (see gun rights in the US, Brexit in the UK, very polarising topics which can always be trusted to start an argument). Initially there are the economic differences, caused by provinces, which are designed to make large empires hard to manage, but I'd like to allow the clever player to find their own. Voting in an unpopular sovreign, for instance, can shatter a nation, and so a player should be able to find an unpopular noble and slowly bring them to a position of power in a foreign nation. Fears, I also hoped, would be wedge issues. A person near the Unholy Flesh could fear it, but the nobles far away would fear their neighbouring socities more. You could then cause them to argue over who is the major threat, until their society collapses due to inability to work together. Make wedge issues a thing the player creates, rather than just a set of default conflicts.
The rest
With regards to the rest, though, I agree. The clue system is different, and plays completely differently. This is simply a change in how I felt the game would best be played. This said, in previous versions there used to be "world panic", which allowed nobles to feel fear on a global scale, and respond collectively, unlocking new abilities in response to the growing threat. I believe I'll probably re-implement that capability at some point, bringing in some of the desirable features of That Which Sleeps.
And yes, the Lovecraftian aspect of the game is not really reflected in the mechanics. Madness and fascination, forbidden knowledge and dread realisation, I would love to have these in game, but must justify them in terms of how fun and balanced they would actually be. I'd like to push a bit harder in favour of it being Dark vs Neutral. I never intended the nobles to be in any way good people, they are politicians who argue constantly about their own petty concerns, and the fact that they occasionally accuse political rivals of witchcraft despite zero evidence is an intended feature.
Anyway, thanks for taking the time to comment, it was an interesting insight into the game, and it's flattering you took the time to consider it in such depth.
And, like you, I'd very very much like to play That Which Sleeps one day, if only it were possible. Who knows, possibly someone will take the Shadows repository and completely re-work it into playing like That Which Sleeps might have. One of my hopes by making it Open Source is that these gameplay avenues I'm not taking could be explored by someone else.