I am going to say that any nerf to the Harvesters needs to be meet with an equal buff to the Fallen Spire Hab centers. I have seen Fallen Spire fleets costing as much as an Ion MKV die to just Special Forces. And they take long enough to rebuild as it is.
I am going to go for something that I don't think need a Nerf per say, but need a rework.
*Nomination for rework: Warp Counter attack Posts.
I find that these are more annoying then anything else. If they don't hit a Homeworld, then you don't really need to rush back to them as any defences you left on a world you care about (advanced factory, fab or whatever, should be able to take out the attack), and if they do, you basically need to pull your armies back home, sit and wait for the attack wave to come in, then leave and go back to what you where doing. Normal waves you can control where they end up with Warp gate raiding, you can't control where a Warp Counter attack wave hits, save for building Warp Jammers on every planet as it command station and that only makes certain that they will go for the homeworld.
I would really like to see this changed in some way, to make it much less of a ok, fly back and protect that planet, then go back to what you where doing, to something a bit more exciting.
I however am not sure how exactly to do that.