[PvK]

No, that's what I mean - assassins and ninja in SE4 would be intel ops and maybe an intel facility, rather than ground troops. The ground troop equivalent would be elite infantry (although generic).

It would be easier to list what does work than what doesn't in ground combat. I don't think cloak would have any effect. Allegiance Subverter ability I don't think would work, since it doesn't work against fighters, but I heard boarding parties can work on drones, so that ability might allow you to get an Allegiance Subverter troop weapon. I hope phased weapons work, but I don't know. I doubt armor-bypassing would help. A lot of that I have not tested, because so much was not working when trying just to get the basics to mod.

For air units, I think it would be a new troop vehicle "size" (to get a plane picture) probably using a flight system component, which would have some to-hit and mods that can stack with armor and infantry, to add a third type that is good to have all three of (thus, the side with air superiority gets the bonus for the whole army, and denies it to the enemy by taking out their Last air unit). It may (or may not) be tricky to make it so you can't put the flight component on an AFV to get a tank-type unit. It would probably be best if there is a way to limit their firepower against ground troops and vice versa, but make them most effective against each other - probably need to use shield-bypassing and/or armor-bypassing, or maybe engine-destroying, or something, to get that to really work, if it's even possible (sounds like a lot of trial and error and testing and tweaking).

Armor is handled by small/med/large "Troops" with armor and/or shield components.

Mech inf is small "troop" vehicles with light or low armor combined with infantry.

I'm not sure what you mean by "mobility allowed cav" - if you mean that armor and mech inf have an advantage because of their mobility, I'd say that's abstractly represented in this locationless combat system by their high firepower Ratings. An infantry-only force can't dish out much firepower, and will gain a lot from adding some larger units with good firepower.

I was tempted to add Starship Troopers-like battlesuit mobile infantry, but it seems like that's more of a Foundations mod type of thing (should probably have its own tech area[s]).

PvK