So far I really like the game. But! I honestly think it could be expanded.

How: it is mentioned by the Inquisitor himself: strongholds.

What would they do? Well if you increase the stronghold it could hold upgrades that would for example improve crafting. 

(So far crafting has been disappointing as I got lucky with drops and am running around with a chainsword I go ages ago and everything is less quality ....) .

Or it could "improve system  stability and security" meaning less white missions (hey if you do send an inquisitor out to work at least give him a worthwhile job?) 

Or something simple as during say a mission where you can summon an astartes if the mission is against chaos: you get a Grey Knight

instead (Ordo Malleus), for Tyranids you get Death Watch (Ordo Xenos) and for Heretics/Renegades you get Bolter Bi ... ahem I meant Adepta Soraritas (Ordo Hereticus).

It could also have a small manufactorum that allows you upgrades to say the Crimson Wanderer for missions specific to that. 

Of course the higher the stronghold level the higher the items in the store and the rarer they are. (Like Tarot cards maybe? Because getting those to max level is a grind of EPIC proportions)

Each available subsystem could have one stronghold maximum. And could of course feature missions to defend it. 

And of course make max level in the future 150, allowing us to unlock more passives. 

Anyways good game so far, with my only meh being that added tarots don't seem to work every mission. Which is a shame considering the amount of cards one needs to upgrade all Tarots and that crafting seems to be a bit meh (crusades drop reaaaallllyyy good stuff)