It's certainly bizarre if you go into VI presuming that it has the same meritocratic standard of only including "empires" as V did.
And there was no "theme" connecting the civs in V's expansions like there was in VI. Rise and Fall, the political expansion, included seven smaller imperial or quasi-imperial powers which were well-known for resisting even larger empires (Scotland v. England, Cree v. Canada, Mapuche v. Spain, Dutch v. Germany, Zulu v. Boers, Georgia and Korea v. a lot of people)
This seems very much a case of seeing a pattern because you're looking for one. Most civs can be defined as having fought against rivals, often bigger rivals. While leaders like Robert and Wilhemina were noted for leading their civs in resistance, Seondok wasn't - indeed the main conflict during her reign was suppression of an internal rebellion. That Korea has during its history resisted "a lot of people" is ludicrously nebulous. Poundmaker is notable for actively not taking part in what seems to have been an 'accidental' rebellion that lasted all of six hours. Shaka was an expansionist leader, and wasn't in conflict with either the Boers or the British.
Gathering Storm, the terrain expansion, included seven civs with terrain bonuses known for thriving in extreme frontier conditions (Canada and tundra, Mali and desert, Maori and ocean, Phoenicia and coasts, Inca and mountains, Hungary and rivers/hot springs, Sweden kinda shoehorned with multi-terrain bonus and open air museums).
As I noted, just like Civ V expansions the Civ VI ones focused on mechanics new with the expansion. You're on firmer ground here but are misreading the reason - mechanical, not some overarching pre-planned theme. There's no good thematic reason to associate Hungary with rivers and hot springs (and conversely the Netherlands was a terrain-linked civ in an earlier expansion, and Egypt liked floodplains), it was just a way to show off mechanics.
Both expacks had a generic domination civ, probably for balancing purposes (Mongolia, Ottomans)
And this is just handwaving. There's no reason the expansion that included the Zulu and a domination-focused Mapuche needed another "generic domination civ", you're just creating a new bucket to explain why Mongolia doesn't fit your pattern rather than accepting that the pattern isn't real.
The question is not whether VI had greater design plans in mind, because it clearly did.
No, that isn't clear at all. I suspect they had firmer plans to stay with a two-expansion model than Civ V did, simply because it's not clear Civ V was ever originally conceived as having full expansions rather than DLC content - but I don't imagine they had any specific plans about the themes those expansions would cover or the civs they would include. They ended up in retrospect with some omissions the fanbase found unexpected, not because of pre-planned further content, but precisely because they hadn't planned far ahead and simply found that Babylon et al. didn't fit their needs at each stage when they had content to add.
Ending up doubling Canadian civs while missing civs people expected to see is precisely the sort of thing I'd imagine happening if the content was planned on a pretty ad hoc basis as it went along.
The Mapuche were not imperialistic and equally represent Chile.
I think your imperialistic/non-imperialistic division is completely invented. Yes, the Mapuche are probably taken to represent both Chile and Argentina - not because of map representation, but because of the demographic criterion: they appeal to both Chilean and Argentinian players. Culturally they don't represent either and instead represent only a single, Mapuche culture. They aren't varying cultural representation any more than any other single civ. As your map indicates, they had a very small geographical coverage compared with Argentina.
They also happen to fill out New Zealand pretty elegantly on TSL maps, giving us a Polynesian civ that could actually have land to work with as opposed to Tonga or Hawaii.
That's purely a gameplay consideration - New Zealand has usable land that the Polynesian islands don't on a TSL map. Also, as implemented, the Maori don't even start in New Zealand and when played by the AI don't seem to end up there, at least not all the time - in my last TSL game they ended up in Japan.
No it wasn't. Carthage in V didn't have a writing bonus; it makes sense for the Phoenicians but not for Carthage. Same with the cothon.
The original meaning of 'cothon' was the harbour at Carthage - it was a proper name like the Pharos in Alexandria. The cothon was also the unique building for Carthage in Civ IV. How is that not appropriate for Carthage?
A eureka for writing specifically is a slight stretch for Carthage, but representing the Phoenician alphabet as a Carthaginian ability makes sense as it was the area that continued to use it for longest. I'm not suggesting they didn't want to represent other aspects of Phoenicia with the civ - what I'm pointing out is that Carthage has always been the game's representative for Phoenicia as a whole (other than in Civ V, where the city state mechanic allowed them to represent the independent Phoenician cities as city states).
As I stated above, the civs were themed to the expacks. So Netherlands got a loyalty effect because there was design synergy for a civ that was already likely going to be included because POLDERS.
Ah yes, polders - the terrain-linked improvement that by your logic should have resulted in them being held for the next expansion rather than the imagined "anti-imperialist" theme (how does that theme incorporate areas like the Netherlands that have been major empires and subject states alike?).
Again, you're looking at it backwards: the Netherlands would have been a good fit for the base game or either expansion. At some stage Firaxis decided to put them in the first expansion, and made an ability that fit, rather than hold them back just in case they needed a loyalty civ or a terrain-linked civ for an expansion. That logic would have prompted them to hold England back for similar reasons.
That isn't any different from Civ V putting Byzantium in its religion expansion, for instance.
I guess I just need to keep posting this every ten pages or so because nobody goes back to read how we got here.
More pertinently you need to do a better job of explaining why a map with gaps fits your imagined scheme more than Firaxis' own stated intent and past practice. Why are the North American civs all clustered in the east? Why is Central and southern, and most of West, Africa empty when we're about to get Ethiopia - a civ directly continuous with Egypt and Nubia in East Africa? Why stick the Mapuche in to represent a small stretch at the 'waist' of South America and leave a large Argentina-shaped gap (actually larger than shown because the Inca seem to reach too far south and Brazil too far west). Where do you imagine your Bulgarians fitting as there is no space at all in Europe south of northern Scandinavia? Why, indeed, is Ireland empty while Great Britain has two civs?
Courtesy of reddit /u/derPhilstift (red non-Spain blobs are large unfilled regions with potential). Look at how cleanly continental Europe is filled by Hispania under Philip, France, Germany, Poland-Lithuania, and Hungary. Aside from a couple LARGE sprawling empires like Rome, Macedonia, Phoenicia, to some extent the Ottomans and Mongolia (which are comfortably represented by modern Turkey and Mongolia), every civ has been localized and culturally vamped up to eleven to cater to modern nationalist sentiments.
Civs have been 'localised' because Civ fans, myself included, have complained for years about blobs. 'Nationalism' has nothing to do with it. They aren't appealing to Cree nationalists by not having a "Native American" civ.
They added a whopping TWO civs to the tiny South American continent, just to fill out as much geography as possible.
Because of TSL concerns - South America has always been underrepresented, and having only one or two civs for such a large area leads to an easy start without competition for anything that spawns there. The way TSL civ generation works, not every civ is always present anyway (the only unmodded TSL map can have only eight civs), so more South American civs in the game increases the chances of having at least one. In general TSL is skewed by the odds that nothing will spawn in the New World, so there's a need for more American civs for the region as a whole - not just South America specifically. Conveniently, this is a further justification for Canada.
nor Argentina under Eva Peron, a "big personality" and a female to boot.
Likely too recent and, I think, controversial in-country. General Rosas also not popular despite being a good option otherwise.
We got...the most you could possibly fill out South America with four civs.
Which is what you want for TSL representation - you don't want a Bolivian native civ when you're using the Inca with a capital in southern Peru. Argentina would have worked, and has more viable leader options than Peron, but Brazil is already there and represents a post-colonial civ. Likely the original plan was not to have multiple post-colonial civs in either South or North America, as Canada seems to have been a late decision and I suspect nothing in New Frontier was planned at the time the Mapuche were introduced.
Just because the devs have other express design goals does not mean that they can't have implicit design goals, or that any of these need be in conflict.
Occam's razor would suggest adopting the simplest explanation, which is that the goals the designers have announced are the ones they applied, when this satisfactorily explains everything we've seen. There's no need to invent patterns or motives that aren't there.
And Ireland was never an empire. Scotland briefly held overseas territory
Yet again, you're turning civs into whatever you want them to be for the purpose of the moment: Scotland was in Rise and Fall because of its resistance to imperialism, but favoured over Ireland because of its (very short-lived) imperial adventure. It's amazing what patterns you can come up with when every civ is what you need it to be for any given argument and all counterexamples are ignored.