Ideally I would want a mix of DoW 1 & 2, if we were playing Imperials anyway, with large battles, fortifications, turrets, and chains of supply similar to CoH 1. This would be the battleground of the Guard however, mass battles with artillery, air strikes, armour and troop deployment. Maybe on the bigger maps and later scenarios even Titans striding over the battlefield.
However in contrast to this i'd also have small covert or strike missions with Astartes or Assassinorum operatives, to assassinate leaders, to seize relics or tech, to scout out enemy positions, to reconnoitre space hulks and maybe even infiltrate enemy strongholds. Indeed you could have almost a dungeon crawl, and make a little RPG out of it. However I would have small, expert teams operating in these missions, with no back up, little to no reinforcement and a very real chance of failure.
Perhaps there could be teleportariums or small Imperial outposts on maps, where one can heal up, re-supply and gather intel. Or maybe even bring critically injured members back to health, teleport them back to the medicae facility, or see them entombed in a Sarcophogus if too grievously injured. Dragging ones comrades back to such places might be a nice strategic choice, you either leave a valued, expert team member behind and lose all his experience, or you risk being gimped by his body as you drag it through the map to a point where he can be brought back into play in a later mission. Then you have to decide whether or not to press on with a smaller crew, or abandon the mission and take the consequences.
That's another point where i'd focus, consequences for lost or abandoned missions.
I can imagine a basic scenario as say a covert planetfall with elite forces, silently seizing strategic points such as a spaceport, scouting out opposition, assassinating key leaders, monitoring enemy transmissions and preparing landing points for the incoming troops and materiels. Perhaps as a last objective a number of coordinated distraction attacks.
The second part would be the strike forces planetfall, perhaps first an orbital strike to clear the area of the enemy highlighted in the last mission, Valkyrie drop ships delivering troops, larger vessels delivering tanks and artillery, ammunition dropped or collected from the enemy, all based on what has been achieved in the previous mission. After this there would be a limited time to reinforce ones position, have the troops entrench, the tech priests set up defences, the commander issue orders and decide on battle lines, the armoured sections be deployed etcetera. This would culminate in the battle.
Perhaps during this conflict the attention could once again at some paused point focus on the initial strike team, as they are tasked with another covert mission arising from the commanders grasp of the enemy, and this could affect the larger battle in some manner when we switch back to it.
Probably all too ambitious and impractical however.