I just started it again and found out that you replaced the mercenaries with towers and drones ... not sure if they have the same issues I had with the mercenaries ...
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The new turrets and drones were designed specifically to try and fix the issue you mentioned with the mercenaries since I have gotten many similar complaints about it. They now cost ore directly instead of money, and much of the game has been rebalanced to encourage a more active play style and rely less on permanent upgrades.