While there are many major issues with ground combat, I think one major issue is the fact that Gene Warriors are the be-all and end-all.
But are they really?
Let's consider this logically.
Gene Warriors are obviously the best for defense when you can put 12 armies on a planet. In terms of concentration of force, they beat everything except titanic life (which is limited to smaller numbers anyway).
But I can send more than 12 armies on an attack. I can create armies of 100 or more troops for invasion purposes. In terms of economies of scale, are Gene Warriors actually better?
For comparison purposes, let's leave aside species and building considerations. Let's just compare basic unit stats and costs of some units. Let's assume we have used the technology cheat that gives you every non-repeatable tech. (This means we have some techs in place that reduce maintenance costs.)
Gene Warriors cost 350 minerals and 50 energy credits. They take 360 days to build. They cost 0.8 energy credit a month to support.
Slave armies cost 20 minerals and no energy credits. They take 60 days to build. They cost 0.20 a month to support.
Clones cost 60 minerals a month and no energy credits. They take 30 days to build. They cost 0.26 a month to support.
Robot Armies cost 15 energy credits and 100 minerals. They take 90 days to build. They cost 0.40 a month to support.
These stats mean a few things:
1) For the mineral cost of a single Gene Warrior army unit, I could build 17.5 slave armies. Note that the slaves cost no energy up front.
2) For the mineral cost of a single Gene Warrior army unit, I could build 5.83333 clone armies.
3) For the mineral cost of a single Gene Warrior army unit, I could build 3.5 robot armies. For the energy credit cost, it's 3.333333. (Close, but not quite the same.)
4) In the time it takes to train a single Gene Warrior army unit, I could train 6 slave armies.
5) In the time it takes to train a single Gene Warrior army unit, I could train 12 clone armies.
6) In the time it takes to train a single Gene Warrior army unit, I could train 4 robot armies.
7) One Gene Warrior army costs as much as 4 slave armies, 3.07 clone armies, and 2 robot armies in terms of maintenance costs per month.
Alright, so if Gene Warriors are going to be worth building for offensive purposes, they need to beat out these other unit types.
With all non-repeatable techs, researched, here's the damage break down:
Clone armies: Average damage: 2.94
Slave armies: Average damage: 2.71
Robot armies: Average damage: 2.59
Gene Warriors: Average damage: 7.085
Health:
Clones: 250
Slaves: 230
Robots: 400
Gene Warriors: 600
So, in terms of DPS, Gene Warriors are worth 2.4 Clone armies, 2.6 Slave armies, and 2.73 Robot armies.
In terms of health, Gene Warriors are worth 2.4 Clone armies, 2.6 Slave armies, and 1.5 Robot armies.
So, without factoring in morale, Gene Warriors are not that great of a buy. They take too long to build, cost too much, and cost too much to support.
What about morale and morale damage?
Gene Warriors have 400 morale and have an average morale damage of 14.175.
Clones have 250 morale and have an average morale damage of 3.6.
Slave armies have a morale of 200 and have an average morale damage of 2.715.
Robots have a morale of 200 and have an average morale damage of 2.595.
So, if we care about morale, Gene Warriors have the morale pool of 2 slave armies, 1.6 Clone armies, and 1.6 Robot armies. In terms of damaging morale, Gene Warriors perform as well as 3.9375 Clone armies, 5.22 Slave armies, and 5.46 robot armies.
What does this mean?
In terms of mineral cost upfront, slaves are a much better buy than Gene Warriors. Sure, you need 6:1 odds to make winning almost a certainty, but so what? I can build 17.5 slave armies for the cost of a single Gene Warrior.
Clones are also a better buy in terms of minerals. You need 4:1 odds to ensure a win (beating both morale damage and regular damage), but so what? I can build 5.8 Clones for every Gene Warrior.
Robots are a loser in terms of mineral costs compared to Gene Warriors in terms of damage (their low morale and morale damage stats really hurt them). But they have better health pools than Clones and Slaves. In terms of unit health, however, they are still a pretty good buy compared to Gene Warriors. They will certainly last longer in combat per point of minerals than Gene Warriors.
What about maintenance costs?
In terms of energy credit costs per month, Gene Warriors seem to beat Clones and slaves. Since one Gene Warrior army costs as much as 4 slave armies, 3.07 clone armies, and 2 robot armies in terms of maintenance costs per month. But Gene Warriors also cost 50 energy credits to build, so that translates into 192 months of maintenance for a single Clone army or a whopping 250 months of maintenance for a slave army. If you build 6 slave armies (to be able to beat one gene warrior per our earlier analysis), it would take 41 months before the maintenance cost of Gen Warriors starts letting them come out on top thanks to the initial 50 credit cost. For clones, it would take 40 months before the energy credit savings of Gene Warriors kicks in.
Then there's the time factor. I could just not bother building troops until I actually need them (to save on maintenance costs). In the time it takes to train a single Gene Warrior army unit, I could train 6 slave armies. In the time it takes to train a single Gene Warrior army unit, I could train 12 clone armies. In the time it takes to train a single Gene Warrior army unit, I could train 4 robot armies.
In short, if time is a factor, I can put more DPS and health and morale and morale damage into the field to fight if I build something other than Gene Warriors. Even better, clones train so damn quickly that I could literally start with zero army, and within a year, I could have 48 clone armies ready to go if I just put four clone facilities on four planets and then didn't bother to build armies until a war broke out. The credit savings for "on demand" clone armies would be substantial for empires that spend a lot of time at peace.
What about revolts?
If you are a slaving and conquering empire that does not suppress factions, you need garrisons on basically all worlds. Here the Gene Warrior might earn its pay. You only need a few to defeat slave revolts, and since those garrisons will be there for decades, the maintenance costs really make a difference.
So, I think the answer to this thread is "Gene Warriors are not top tier." I'll stick to clones and slaves except for defending the absolutely most critical worlds. Or for repressing my slave populations.
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