Personally I find myself disagreeing with some of your assessments, but then again those have to do with what I expected from That Which Sleeps and not so much with Shadows Behind The Throne itself.
Consider this:
"Failures are those which add complexity without a very strong reason to exist. Cities don't need to be constructed building-by-building, as this just adds design overhead. Investigators don't need to go from city to city, this only made the map a confusing mass of units moving. My initial aim for investigators was a vision of a game in which your enthralled lives in a dark castle past a forest, and kills off anyone coming to visit, isolating their village from the world, trying to stay hidden from the world at large as they built up power. Sadly, this just isn't feasible with the current map setup, and the map can't easily be changed without altering all other gameplay loops."
The biggest issue here is that the mechanics you were going for are meant for a different thing altogether. I like the idea of city buildings, I really do, and part of the fun expected from TWS no doubt was taking isolated territories, turning them into fortresses of darkness, and then launch massed assaults on the frontiers of civilization.
And strategies like that is where TWS and SBTT differ the most. TWS had (or intended to have had) features that balances these different approaches out. For example, if I wanted to the above, then I did not need to worry about the nations of the world merging into a gigantic superpower nation capable of taking on all my combined armies by themselves. Sowing mistrust and causing misdirection is easy when the game takes a cue from, say, CK2 or EU4 and you have different cultures and religions - and this applies to both lore and gameplay. Why should I care about some distant threat with huge armies when right at home there is a potential risk of heretics rising up? Why should I team up with infidels to defend their borders when it would be easy to pick up the carcasses of their empires and spread my own faith (and potentially culture)? Even in real life threats like The Huns or Mongols were not enough for the various nations to set aside their differences and work together for a brighter future, and even if they had inevitable issues would have arisen as a result of such strange alliances. Hell, if anything the actions of the Huns basically struck severe blows to the greatest extant empires by exacerbating cultural differences and resource shortages, and the Mongols did basically the same.
Consider the 'clue system' vs. the 'evidence' approach Shadows has. Shadows has none of the above features (this is not a criticism or derision - merely laying out information), and the ones it does have do entirely different things. 'Evidence' is not meant to indicate that a greater threat, the nature of which must also be investigated, is looming on the horizon. It simply means that a noble is dealing in sinful acts that must be punished - lo and behold, this is exactly what happens in the game. 'Threat' carries no weight beyond 'danger'. Hence when summing up whether to team up with mortal enemies or not, nobles often choose to completely set any personal ambitions aside and join up with nemeses to defeat the player's forces. Clues on the other hand were explicitly not about the player's servant at all (who would accrue 'fame/infamy' overtime simply by performing actions too often/too great in power), but rather about the nature of the player's character. This is why in TWS's intended gameplay performing actions not expected of one's character was meant to be a good way to throw off heroes - hey, it turns out Karth (in TWS's lore the creator of Orcs) was not behind this game's manipulations, despite orcs being pushed to attack civilization over and over by eldritch forces.
Finally, consider your vision vs. potential playstyles. In-game tools provided, Not everyone is going to go for Dracula. Not everyone is going to for Deep Ones or Orcs either. Some will love political manipulation, others will hate it. Ultimately what you need to do is think what you want your game to do - not what you want the player to do. So far in SBTT what I have seen is a classic Light vs. Dark thematic centered around nobility, all eldritch elements have come second to it. Hence what you might want to do is either keep expanding things or rework the way your existing concepts interact with each other (for example you could make the 'Dark' faction more akin to stereotypical demons, even if you keep the Lovecraftian lore, as those would be more suited for a game based around court intrigue... With their contracts and infiltration and all that).
All in all I am glad that work continues on the game, but I just wanted to say the above the above to offer my perspective.
Edit: Also please excuse the language but damn, the itch.io interface still confuses me after all these years.