Not a Warhammer 40K expert so I think that makes me perfectly capable of proposing a Warhammer 40K game.
An WH40K set RPG style game that's party based, with your main character being a Commissar. I'm thinking it'll be a party based game kind of like KOTOR or Dragon Age but the game will have an isometric view for the most part. I'd like combat to be in the vein of something like X-Com or Final Fantasy Tactics so it'll be turn based and likely off of some sort of initiative. It'll have a big and thick companion, morality and loyalty mechanic.
The basic idea is the main character is a veteran and senior level Commissar returning from some sort of successful campaign against Xenos scum or whatnot and he's part of a large force that is then dispatched to a very important and built up world that is under rebellion. So the opening scene will have the Commissar helping lead an assault on the Governors palace and battling their way through the traitorous local PDF's and palace guards or whatever nonsense and executing the Governor and after that engaging in the various thick moral and world affecting choices.
For a main basic morality meter, it'll be between a metaphorical Radical and Puritan (of course) even though he's not an inquisitor, the game will be kind of treating him as a Diet Version of one. The Radical Faction will be represented by an Ordos Xenos Inquisitor (perhaps one who directed the campaign prior to this game) such as a Helynna Valeria type who wants to seek out xenos technology and use it towards their own ends. The Puritan Faction can be represented by a Canoness of a Minor Militant Sisters of Battle Order or a Preceptor or Commander level type so we can avoid some sort of Inquisitor v. Inquisitor type of schism trope.
Plus the idea is that both sides are still working together. The primary focus of the story will be rebuilding a 'Schola Progenium' on the world with secondary missions including establishing a new government, purging the hive cities and local bureaucracy of traitorism and wrong loyalties, and securing the planet against future xenos threats (it can be a border world somewhere). There'll be a lot of moral choices involved here.
Such as when dealing with Hive Ciites, you could support the Puritans by empowering the Adeptus Arbiters/PDF's/Enforcers in securing the Hive Undercities or gangs, or the Radicals in setting up networks of informants and scouts and guides and controlling the Hive Gangs from within instead of externally.
You can help establish a new Planetary Government. Maybe a Priest was a member of the Royal Family and led the Faiths Militant in rebellion against his own family and supported your initial assault on the Palace. The radical option would be placing a more independent leader in charge of the family of another noble family that will be beholden to the Ordos Xenos inquisition.
Maybe there's a threat of Dark Eldar pirates from the Webway. The Puritans want to find them, burn them and cleanse their Webway hovel and slaughter those that work with them. The Radicals want to find them, burn them and cleanse their Webway hovel and slaughter those that work with them.... but keep the Webway hovel for themselves and extract secrets from any Dark Eldar captives and see if they really are too kinky for torture.
The main narrative is establishing a new Schola Progenium. Since the Commissar is an Orphan who was raised as an Orphan, as was both the Radicla Inquisitor and Puritan Canoness, themes of the adopted family can infuse itself into the story. All three factions want to create a proud new Schola and as Commissar it'll be your main goal to oversee it, marshaling resources and personnel to make it successful and culminate in electing one of your Companions to lead the new Schola under your supervision.
I'd like the Companions to be a diverse group of course. Maybe the aforementioned Priest who led the Uprising against his own family. A Gun Servitor that is found in the palace wreckage that is more then just a lobotomized drone. A Squat mutant whose an ImpGuard veteran that loathes xenos scum since she's suffered the depredations of the Tyranids wiping out her civilization and Dark Eldar pirates haranguing the refugees. A noble who has no future legacy because she didn't inherit the Navigation genes from her family line. A master assassin who works for one of the Hive gangs. Some badass Arbiter who speaks softly and carries a big maul. Maybe like a dozen companions max. Plus you can get distinct ImpGuard companions. A Skitarii Ranger perhaps, or an Inquisitorial Stormtrooper. A gearheaded Tank Commander from Tallarn or a demolitions specialist from Krieg or a scathingly sarcastic and stereotypical Ratling sniper. Do the same with Harakoni or Catachan or what have you etc.
Not sure if it'd be that likely to have actual Xenos companions. Seems unlikely to be honest. He's a Commissar doing special missions, not an Inquisitor who can do what they want for the most part. There might be potential for a Jokaero Smith type, or maaaaybe an Asuryani Outcast, maybe one who previously lived among the Exodite Eldar, but I'd have to think of an appropriate storyline for one to be hanging around on this world.
The more you work with them or through them, that can affect not only their outcomes and that of the planet, but also the Radical or Puritan balance and also because one of them will be overseeing your Schola (if appropriate) and imparting a unique character upon it. Putting a Krieger or Tallarn vet would make it very strong of the Imperial Creed and martial virtues, a Priest would make it more Ecclessiarch sympathetic but less martial because of the Priests background, a Squat or Ratling would make it more strangely more diverse.
And obviously along with leveling up yourself and your companions, you'll get to choose cool wargear and everything. And you can both guide and see how dynamic the ending fates for each of the companions would turn out to be across various playthroughs.
Ultimately the ending for the character would imply they would become the leader of the Schola themselves regardless of what faction they choose, but there can be a hidden narrative that builds up to the climax at the very end. The Gun Servitor found from the very beginning can be found to be possessed by an ancient 'Machine Spirit' and remembers a time many millenia before the Inquisition and the Ecclesiarchy and subtly try and guide the protaganist astray discovering teachings and lessons contrary to the Imperium and Imperial Creed such as the idea of Imperial Atheism and the like. While the Machine Spirit isn't of Chaos itself, it's teachings are clearly contrary to it. The propagandist will eventually have to confront this 'Machine Spirit' and either bring it to the attention of the Ordos Xenos Inquisitor, or the Canoness or deal with it himself. The Xenos Inquisitor will toss the curious creature into a vault for further study and award the Commissar into becoming an Acolyte in her retinue, both to keep him away from the Church and to keep an eye on him for better or worse. The Sisters will destroy the abomination and then submit you to the Ordos Hereticus... but as a potential valuable member of one of their Inquisitor retinues.
Or he can destroy the Machine Spirit himself and choose to lead the Schola as originally intended and make a School that will thrive in its service to the Imperium. Or he can keep it a secret and lock the Machine Spirit away... while gleaning his own secrets from it. A path that can lead to great reward for himself and the Imperium potentially, but far more likely just great risk as such a secret getting revealed would likely have him terminated.
The final choice is likely the most wrong choice. The prior three choices of having the AlienHunter, the Canoness or yourself handle it might also be determinative not just on the Puritan/Radical spectrum but ones companions as well and how much trust and loyalty they have in you. The final choice would require hiding it from all of your companions, that adopted family you've been cultivating through the entire game.
The story does contravene having a crapsack/grimdark ending but I feel that's more of the general flavor and atmosphere as well, not just in having perpetual downer endings. I also kinda want to avoid the Space Marines and strict Chaos storylines because that's such a focus on Warhammer 40K already. The idea of dealing with normal Human Imperial problems seems more compelling and it can still be done on an epic planetary scale. The diversity is less meant to be for wokism and more that games are more interesting with lots of replayability and different play experiences. Each companion can be fairly different from the others and thus lead to different builds, synergies and outcomes.