I played a few sessions with a friend yesterday and today and here are some more thoughts:
Substrate Anti Air
Since the Sky Cleanser is a tier 1 unit, it is far too weak to fight bigger amounts of PHC bombers (Hades) since those are quite tanky.
More than once I had a reasonable amount of Sky Cleansers but one fly by of like 6-8 bombers evaporated them and these bombers went ham on my army until air support arrived.
Quick comparison: Hades 4500 HP for 3 bombers -> 1500 each
Sky Cleanser 60 HP, 28 DPS...
Orbital Jamming facilities
In general a very good idea and a needed hing, considering the might of the offensive abilities. But it was fairly odd that I couldnt even use the scanner sweep on enemy territory. All of the territory controlled by the enemy was ability blocked and it didnt look like they spammed those buildings everywhere.
So the scanner sweep seems pretty useless to me now...
Engineer Drop Down
Really cool to have this ability as PHC but I miss it when playing as Substrate. Especially on big maps it is annoying to build them back at your base and then wait till they arrive at the front.
Or maybe make them buildable in the production buildings? (maybe with a faster tier 2 builder? 
)
Health Upgrade
When you upgrade the health of your units, I would expect all my current units to gain HP both in the current and max HP. This is not the case, only the max health increases. Intrinsically this is no big deal. What really bugs me is that then even new units have not full health when being built! 
Building prices
Since the Substrate builds all ground based unit in one building, this building is more expensive. Sounds reasonable.
The imho big consequence is that the Substrate can't start as fast as the PHC. With PHC I build a factory, extractors, more builders and so on from scratch without running out of saved ressources.
Substrate can't do that since they run out of stashed metal faster, resulting in a slower start.
Build infos
When hovering over a unit, the build time and cost are displayed. Maybe add the impact on your ressource gain rate in braces?
Like
Build Time 90s
Metal: 400 (-5)
Radioactives: 250 (-3)
Idle production facilities and supporting workers
When I let a worker support a building, he does it forever. Even if i stop producing in this factory because the front line is too far away.
Any supporting worker will still be busy "supporting" the idle factory and wont show up as idle.
Extractor size & health
It has already been mentioned, that the extractors are too small. I totally agree.
What bugs me more is that the 10 HP they have is by far not enough. In the early game you can harass your enemy with rushed Pans (PHC scout).
Their weapons do 2 DPS but having like 3-5 of them is enough to kill a lot of extractors therefore massively slowing your enemy in the early game. Ofc this shouldn't work in midgame as AA should be present by then.
