I have an idea regarding late game resources management and weapons.
1 Turn back impossible weapon resources collecting like vanilla rather set amount of weapon. Late game the normal resources like research, material and foods can be use to buy recruits, rebuild heaven in exchange for diplomacy and keep them surviving longer. If we use Etermite setting this help balancing out the difficulty with careful resource management. Just make impossible weapon a bit more expensive and require faction diplomacy access to build it. So you got to spend the vanilla resource to keep bastard happy and let you make impossible weapon with their effects. The idea of the game is tactical battle so make a hell a lot of battle with many tactical choices during combat use weapons we make. To achieve more battles we need more heavens to survive.
2 regarding impossible weapon we can have faction modifications to make variety
For example NJ can make weapon set target on fire or armour piercing, Senadrion maybe Poison or Paralysing enhancement imagine grenade launcher poison a group to pandora; or Sniper rifle with night vision or target able enemies in mist so we can use head slot for mist disperse attachment. For the DoA i dont know maybe Acid effect launcher,acid melee weapons or a free close melee attack ability on enemies engage in melee. Maybe make them specific melee soakers with weakness like very high resistance to acid and poison but extremly weak to fire. Imagine a soldier stand in pool of acid like taking bath but get burn easy. So make like melee armor ability that require DoA diplomacy to make using ancient reources.
That way the game get more challenging and balance out the excess resource build up on late game. You have to spend resources strategically to make the game fun.