-1. a size 1 city has like 50 people in it from past projections. Units start at size 5... a 100-600 people which means a stone thrower that takes say 20 turns on eternity has 4 to 5 times the number of people as the city that spawned it.

It should be size 2 and wander size 1 logically.
In PH and Ancient eras, units build should be much smaller than the normal Group Volume for realistic reasons. I don't think an Era-modifier or adjustment per tech is really necessary (though possible), as units obsolete/upgrade quite fast in C2C.
From a perspective of eventually moving into the Nomadic Start portion of the game we might need to make some adjustments to those population size calculations per/pop point.
I can see the point, however, of diminishing the GV of the very first units: Wanderer down to solo (if it's not already - can't recall), Stone Throwers, Brutes and Tribal Defenders down to Party Size. Then increase their Qualities up even one step further to compensate. Would make sense and would also enhance the progression that suggests that Humans were probably MUCH physically stronger in that era thus a high combat quality even if their weaponry was crude and their group sizes smaller.
I like this idea actually - and it will make getting the first unit level ups take even longer which I've really enjoyed the slight 20% or so average slowdown on xp gain throughout the prehistoric era.
I'll put those adjustments on my list.
-2. I see nothing that says barbs can do this... barbs have no unit upkeeps and get units through spontaneous biogenesis. This means animal and Neanderthal stacks of tens of thousands should end up common doomsday scenarios... in the stone age.
They can't at the moment because no AI can. Are you suggesting they should be able to or should be kept from being given any AI to do so?
-3. Combining three units makes one of them of a greater stack size. National units (thieves and such included) are limited in build count. This breaks all unit limits to comically large proportions. No to mention spilt spamming thieves and making a moat around enemy cities seems the most effective any city strategy. If they have dogs just get a thief unit into the city and sit and split. with one crime causing promotion on your size 5 stack before it splits into 15 puny units... that city is crippled beyond all reason basically forever for like 6 :gold : a turn.
Unless I'm reading that wrong so it means I can split a thief a dozens of times... which means I can do this while in anarchy and mangle their crime level... then fuse back together before I need to pay for them for real.
Criminal units may not split or merge. I MAY have to make it impossible to split or merge Cultural units unless the game is played with unlimited national units. For now, yes, its a way you CAN get around the limit as you observed. My bias against limiting those units in the first place may have had something to do with my choice to not go out of the way to stop them from being able to.
However, I think a simple mechanism could be put in place to deny units that have a limit at all to merge or split if unlimited national units isn't in play. If y'all want it that way I'll be happy to add this check into the canMerge and canSplit checks.
-4. Once you get any kind of unit that can bombard this strategy is basically useless. You can do more damage in less time to the mega unit and it can't heal faster than it can be whittled down.
You say 'this' strategy without specifying which strategy you're talking about. Personally, this is where I think the splitting/merging gets interesting. If you come up with a good strategy for facing bombardment units, let me know.
-5. Simply splitting a unit for a surround and destroy fodder means its easier to drag down a mega unit than to keep it intact. Splitting a unit up means I can use a single caveman unit and surround a 128 pop city and cripple it for the real unit to take down.
I think you're thinking they'll be able to split much further than they can while remaining combatatively meaningful. That -20% for each split really hurts the power of the unit and will invite a LOT of lemming-like sacrifices that MAY not even harm the more powerful city defender. Surround and Destroy may not be worthwhile to split a unit to gain the benefits of since the amount of bonus you get from S&D from a unit that is adjacent to your opponent is based on the odds that supporting unit WOULD have if it were the attacker. So weaker units mean a weaker S&D benefit they'd offer and I believe that you'd find yourself hard pressed to get MORE out of 2 more units to surround with than you would have saved by keeping those units grouped in to the original.
UNLESS you start taking full advantage of some pending S&D manipulating promotions I have waiting in the development wings soon to be produced.
But go and see how it plays for you where that's concerned.
-6. Realistically cities become largely unconquerable with splitting... I can split units to comical proportions meaning I'm having single guy micro units stall out the cities defenses ad infinitum. I doubt the AI will splinter its units to speed things up.
It won't at the moment but it probably should be able to give that consideration. It's also not going to be too challenged to take down those units so each turn you're sacrificing as many of those little guys as the opponent army can make attacks. You'll slow them perhaps but it's certainly putting all the casualties on your side forcing you to send reinforcements while he's lost nothing (probably not even health on his units.) This gives your enemy a production edge as he's not replacing any of his army, just adding to it. While you on the other hand are effectively stalling him out but you're taking actual losses, however small they may seem.
-7. By your upper size unit logic we can solve world hunger by making China and India into a pair of stupid huge conscription units... or even a single conscription unit... at the cost of upkeep only 20% more that the Best Korean army. Technically that goes for the entire planetary population.
We're talking some game logic and logisTICS here. We're also talking about military forces rather than the population of nations. Furthermore, I'd argue that similar reasoning is what makes the vast majority of humanity pool into cities rather than diffusing in perfectly balanced divisions throughout the whole of the nation. Those cities make those people easier to serve as nearly all services may be had there. Shipping and distribution is made cheaper and easier into and throughout metropolitan areas, making food and other goods cheaper to bring to those living in the cities (though they may not charge any different prices so as to profit more in those regions than they can in more outlying ones.)
So in a sense, you're right and it's to some extent happening. It's just that these great city infrastructures take a lot of time to develop and thus cities can only handle so much population growth without becoming a disorganized planning mess. Thus it does not quite benefit us to centralize EVERYONE. Besides... we all have different preferences.
-8 Nanotech swarm is a city sized swarm of at least countless units. That means it gets a bonus of +160% power for numbers and another +80% for size. Does that mean it is a 220(?) times 240%=528 power unit or a comically small 600 nanobot swarm is the equivalent of a Mammoth tank in combat?
The Size of a Nanotech swarm is Fine. The smallest you can get. Size indicates the general size of the individuals that make up the unit, not the mass of the unit once gathered from its Group Volume. Yes, the group volume is large - Trillions. And all in all the Nanotech swarm does balance out to a positive Str and HP modifier when built under this option. But ideally, its great extremes in size and group are going to be its biggest weak point as well. With promos that will make some units get a combat modifier for each size level smaller than it is, a huge unit with such a modifier would easily compensate (think plasmathrowers from robotic units to counter nano swarms.)
Basically, I think your taking things already applied to units calculated into the units power number and divorcing it from itself. In order to do this properly you need to go over each and every unit in the game and calculate them out as they currently are. That means:
-Wanders are GV(1) S(5) CQ (2)
-Stone Throwers GV(2) S(5) CQ(1)
...
-Nanotech Swarms GV(13) S(9) CQ(10)
By using this method you can keep things saner in the numbers. Also as time goes on and unit sizes get larger your going to need to make some upgrade price adjustments... for instance stone throwers GV(2) upgrading to slinger GV (3) should get a discount if you have a GV (3) stone thrower hoard already.
Also, you need to make larger than relevant for the time period units cost a silly amounts of upkeep

A GV (4-5) unit is basically a size 2 or 3 city wandering around at that point in time. This means sprinkling unit cost reduction modifiers throughout the tech tree. Slingers are cheaper than GV (3) stone throwers as the infrastructure to keep such a huge (for the time period)) force operating is hard to fathom The logistics of.
Well that's my 2 cents from a haven't played this yet perspective.
You're close to the way I set this up. I did go through every unit and determined what level that unit would be in each of the three categories. However, I looked at the 5th layer of each category as being 0. Then one less was -1 and so on. Then by adding all 3 together I can see how far off the unit is from being zeroed out (which would produce an overall +/- 0% modifier to Str and HP.) Some unit types I determined to be better off allowing a -1 or other general offset amount but I tried to keep those offsets consistent throughout all the phases of upgrades that those units would go through (not always for the same categorical reasons though... As an Atlatlist (-1 Group Volume), (+1 Quality) steps out of a more crude era and upgrades into an Archer (both medium size)(0 Group Volume), (0 Quality) they still end up with the same overall 0 offset.
Size and Group Volume both affect gold in equal modifiers per level so most mounted units with greater size and lower group volumes balance out pretty closely on the upkeep modifiers. In fact, I think it ends up being in favor of being cheaper units because I believe the size is generally +1, the group volume -2, and the quality +1. This makes them -1 cost adjustment (thus -20% upkeep.) Elephants are another size up but a quality down so they'd balance out at 0.