My perfect Warhammer game... umm...
It would be a strategy game. But not a regular one, no, it would be like a mix of Europa Universalis and Civilization with a tad of Total War in the strategic side but featuring not only a single planet but maybe even hundreds of them, and their respective star systems (ie 10 planets on a star system).
This would be a turn based strategy game, however it would also have with Dawn of War like battles for land and sea battles, and Homeworld, or better yet Shallow Space like battles for the space ones. That's it, a turn based strategy game with real time tactical battles but no base or soldiers construction/building. No command and conquer economy. You fight with whatever your brought and that's it. Maybe if you can hold on for long enough and you call for it, assets near in the strategy map can come in to aid but that's it (lore exceptions withstanding, IE necrons/eldar portalts, demons summoning, etc...)
For the research system, certain factions (Tau) could use one like to the one of Space Empires V, however the rest could have something else, like only finding technology (Imperium and it's subfactions), or through arcane rituals and requirements (chaos, necrons) or whatever have you.
Population and resources would be taken into account and in a local way. No magic piles of resources shared among the infinity of space (lore exceptions withstanding). If you have an adamantium mine in one side of the planet and a vehicle factory in the other side or even in another planet, there must be a way of taking the adamantium from point A to B.
The infantry would be trained and deployed according to lore, not only choose the uniform and weapon load out, but the squad, platoon and company load out. All this templates of course would be exactly to lore.
As with the infantry squads and companies system, an army and fleet load out system should be used, so instead of you needing to recruit everything individually you can have use the templates and recruit whole armies and fleets on the whim of a click, the game recruiting and commissioning the vehicles from the nearest/most suitable/convenient planets, factories and shipyards.
And last but not least, a proper naming system for ships, where you can customize if they get random names (from generic or custom lists), numbers or both, and their class and design type are also made clear and if any or all of this is written on the hull or not, or displayed on banners and whatnot. The same go for army naming, specifically for squad, platoon and company levels.
Graphic wise I would not be much concerned. Something along the lines of Dawn of War level of graphics would be nice but I would be happy even if is something in 2D, however I have heard that even when 2D is less demanding to the machine, quality 2d graphics (Starcraft 1, Age of Empires comes to mind) are actually harder to make than 3d.
And of course put every race in. EVERY SINGLE ONE!