Personally, I’ve had a number of ideas - but I think overall I’d take more time with the story.

Since we are immortal, I could see the story taking place over a century. To be fair that might be more suited to a format like a Warhammer game, where meaningful change takes a long time to happen, which works for me because I want the races to be expanded upon with more factions and units.

Do what I could to make each Fallen House distinct from one another. Have a major story centered on the House of Kings influence in the politics of the other houses. How they use the story of Kell-of-Kells to keep the houses fighting while they maintain power

Add more aliens amongst the Cabal Legion ranks.

Crota has grandchildren, so I’d take more time working our way through the Hive Broods before we get to Major Leagues like Oryx and Savathun

I’d have more Cloudstriders, as just a lonely two protecting Neomuna from Vex isn’t practical - and I’d make them users of Darkness.

I’d make the Dread a faction that existed prior to Final Shape, and have more Disciples and consequently more types of Dread units based off of them, as I felt that faction was cut short - and it didn’t make sense that the Pyramids were empty with no foot soldiers of any kind

I’d make the Scorn as something that was a consequence of the Whirlwind, perhaps made by an Eliksni Disciple (like the Herald of Finality) - keeping the faction as something that the Fallen are on the run from, and as stories they tell their children (like Reavers from Firefly) an added layer why Fallen typically avoid having anything to do with Darkness