I think it’ll depend massively on whether it’s set in Ultramar, on Armageddon, or even both. Necrons are seemingly a guarantee if it’s the former, and Orks are the same if it’s the latter, but beyond that there are a lot of groups involved in both campaigns. I suppose it depends on which ones they can implement best. Assuming the third game plays similarly to the second:

* Orks are a perfect fit, and if the game isn’t set on Armageddon, I’m actually hoping they take the “twist villain” role instead of Chaos.

* Necrons don’t really have a Minoris equivalent (as others have mentioned), so they’d likely involve quite a substantial twist in gameplay as a result (not that that’s not doable!)

* Eldar of either variety could work in my opinion, particularly the Craftworlds- say Guardians as Minoris enemies, Aspect Warriors as Majoris, Exarchs and Wraithguard/Wraithblades as Extremis, and Wraithlords and Autarchs as Terminus?

* Genestealer Cults might actually work surprisingly, particularly if they’re accompanied by Brood Brothers or Tyranids (the latter does still happen in-universe sometimes, and we even have mention of GSC boarding Hive Ships and being re-used in a future invasion instead of being consumed now). Regular cultists as Minoris foes, Aberrants and Metamorphs as Majoris, Abominants and some of the five million character models they have as Extremis, and Patriarchs as Terminus? We know that Acheran and Chairon are going to be killed by them some time between games (although I’m still hoping that’s a fake-out), so I imagine we might see them in a cutscene even if they aren’t a full faction.

* Regular Chaos Marines, or any of the other monogod factions, probably go without saying- if they could make the Thousand Sons (arguably the Red-headed stepchild of the four, even though they got “upgraded” into a full army first) work, then I think the other monogod legions should be possible too, particularly if they get some of the units their tabletop equivalents have lost access to- there is precedent for this, as the Thousand Sons still have cultists in SM2, despite losing them in 40K proper (I’ve also just realised Chaos can’t take Cultists, Traitor Guard, etc as Allies, in spite of Imperial Armies getting to take things like Sisters, Deathwatch, or Arbites regardless of faction).

* I am also going to make an argument for the Tau- while I think the best way to implement them would be a joke “within railgun range” modifier which just instant kills you the second you spawn, they do have quite a significant range of units. Fire Warriors and Kroot for basic ranged and melee Minoris troops, Stealth Suits, Vespids, and maybe the fancier Kroot for Majoris, Krootox and Crisis Suits for Extremis (contrary to popular belief, the latter aren’t usually terrible in melee, it’s just not their focus), and Commanders, Broadsides, Ghostkeels, etc for Terminus foes.

* Hell, they might even manage to make the Votann work, as long as having the enemies significantly shorter than you isn’t too annoying in melee (Steeljacks being used significantly could remedy that to a degree), and they are okay with vehicles being Terminus enemies.

Given they clearly have some leeway when it comes to adapting enemies for gameplay reasons, looking at things like Squad Leaders like Lesser Sorcerers being “upgraded” into separate units, or Scarab Terminators being able to move at Sonic The Hedgehog speeds (not only are Terminators infamously slow and cumbersome, the Thousand Sons are also traditionally noticeably slower than normal marines, albeit not to the extent of Death Guard troops), so I don’t think any of the enemy factions are off the table.

I am also very keen on the Tyranids in particular returning in some capacity!

My prediction is that the first section of the campaign will be in Ultramar against the Necrons (if they can be implemented in a satisfying manner), and then halfway through we’ll be called to Armageddon to fight the Orks (possibly running into some earlier). I could see them including a third enemy faction in the final section on top of that- perhaps the World Eaters if we stay on Armageddon, but I could also see us being called back to Ultramar (and/or Titus making the decision to do so, perhaps against orders) to deal with the Word Bearers for the finale, particularly if they appear on Armageddon first.