For a millennium, three opposing forces of humanity have fought a bitter and bloody war over their conflicting and unwavering beliefs. There is no room for compromise. No room for mercy. No room for anything but the complete eradication of all opposition.
A few mods that will add resource upgrades for your commander and will provide a strong(er) enemy base, so the enemy is more of a challange. Mod 1: extra upgrades for the commander (resource). Mod 2: enemy has a strong base.
The commander is a bit useless in the later game... I've added a mod that gives it 15 stages of resource upgrades (starting small, but up to 1000 mass/s at level 15). It also adds 5 engineering stages, so that the commander becomes a very powerful builder and powerful in general (more health and regen rate).
A few other mods adds buildings, units to the enemy base. The AI doesn't build much of a defense, this creates a better defense.