Here is a list of what I believe Command and Conquer 3: Kane’s Wrath can teach HW2.
More units: I love HW2’s simplified unit list, but sometimes x4 for each building just doesn’t cut it. GDI has Mammoth Tanks, Predator Tanks, (Zone) Shatterers (hover tanks), Rig Battle Bases, and so many more vehicles that allow for more diverse combat. Ditto that for Nod and Scrin. On top of that, GDI, NOD, and Scrin all have two additional subfactions (9 total factions) that have specialized units (example: ZOCOM replaces Zone Troopers with Zone Raiders)
Not saying Halo Wars 2 has to copy this exact formula, but maybe Cutter should have specialized ODSTs from the main building that have Combat Tech and everyone else can have standard Marines (still keeping their upgrades, of course, but ODSTs lack Combat Tech making them arguably worse)
Free Build: This would break the game, so maybe Halo Wars 3? In other games, you can build your base ANYWHERE on the map.
Toxic Zones: In C&C, there are areas where your infantry can’t go unless they wear special armor (Tiberium Field Suits or Zone armor for GDI, Marked of Kane have a special troop with some kind of armor that allows them access to these areas) or unless you mine the area with Harvesters, or blow up the Tiberium with whatever you have. I’m not advocating for X, Y, or Z here, just the poison area effect.
Leader Powers: You know how Halo Wars 2 has the small problem of players turtling? In Command and Conquer, you can just drop a nuke on them (after 7 minutes, of course). The Ion Cannon is similar to Atriox’s Eradication, but more OP.
There are also some maps with tactical advantages that you can capture with an Engineer, such as EMP stations, defense turrets and mutant hovels. Halo Wars 1 did this as well, with Sentinel Factories and Mega Turrets on some maps.
Transports: 343 did good by adding in Pelican Transport, Mastadons, Teleport and Phantoms. But sometimes that just doesn’t cut it. The Hammerhead gunship is standard to all GDI factions, it can hold one infantry squad and can be used to quickly transport them. Nod has the Reckoner. Scrin has nothing, but can use wormholes.
I suggest letting the Nightingale have a troop bay upgrade. It lets Pelican Transport keep it’s use, but also makes it so you can transport a few troops to far places quickly.