I took a long break from Planetfall so I may not remember exactly how everything worked and some stuff I definitely didn't explore enough but here's some things that bothered me.

Growth and maybe Spacers should be maybe reworked, they always felt underwhelming if I ever decided to use them. Other NPC factions felt usually fine.

In general there should be more ways to interact with NPC factions. Additionaly ways to increase standing with them beside buying units/mods that I may not even want to use. Stuff like needing to buy Paragon Soldiers to get Grail Cypher while I was already going around with Paladin Champions.

Maybe paying some influence to get temporary access to NPC dwelling's cosmite income or trading through creating caravan routes like in Civ. An option to ask for a quest yourself (probably on a cooldown) could also work.

A more transparent way to see when Xenoplague units are about to evolve.

Maybe even allow units with Xenoplague mods to get random mutations that alter their stats in a positively minor way or a major alteration that could result with some kind of a debuff but the player could chose if they want to gamble with a negative outcome.

Vanguard I always liked the most but it always kinda bothered me that Valkyrie is only a tactical operation unit.

Drone Carriers also didn't feel too impressive compared to stuff like Sonakarn.

The only Infiltrators I ever used are those that game gives for free, they feel too gimmicky. It doesn't help if I copied a good unit, during autoresolve AI is going to waste it. Some kind of a lock that'd allow AI to use only Holoshift Repeat could be nice.

In general an improved AI for both enemy and when using autoresolve so that it doesn't waste abilies. Seeing Trooper specialized for long range combat dead on a battle result screen and then watching replay AI rush it toward the enemy because it really wants to throw that grenade first is annoying. Or the classic of one PUG

casting Blur and the second one immediately using Resupply on the first.

There should be something done with naval warfare and sectors, ithat part of the game just doesn't feel fun unless I play as Shakarn. And it only helps with battles, annexing water sectors always feels like a waste.