I'll offer a counterpoint to your argument above: to me Athkatla was basically the finest city hub we'd seen in an RPG... Up until Neketaka. To me Neketaka isn't a problem in the game, if anything it is its biggest virtue; yet I see your post is less about an Athkatla/Neketaka comparison so I'll leave that for another topic, as there's much to discuss here already. Anyways, I feel that you are ignoring a lot of the aspects that grouping the warring factions in a single city add to the overall conflict and depiction of themes and so on. The conflicts surrounding Neketaka isn't just one of interest, it is likewise a cultural clash, and whilst we see plenty of it all across the Deadfire it is never clearer than in that single place where all cultures are constantly interacting with one another and melding, not just at an interpersonal level but right down to the fusion in architecture, aesthetics and the likes. There is a tension to the design of Neketaka that is not merely apparent in the dialogue and interactions, but in the city's construction, layout and aesthetic itself, which would never have had the same effect were we to split the influence of every faction evenly across the different smaller towns. For that specifically we already have a representative settlement for each, in the shape of Port Maje, Sayuka, Dunnage and Tikawara - what tensions and conflicts there are to explore in each I feel are handled solidly too, from the Huana camps in Sayuka to the history of conflicts with slavers and isolationist tendencies in Tikawara, and so on; and much as you propose in your alternative, I feel these already showcase perfectly the philosophies and worldview each faction holds.
There was also a practical reason behind the presence of one big city opposite to multiple, from a production standpoint, which the devs spoke of a fair bit during production. As you probably are aware of, the first Pillars had two big city hubs opposite to a single one, in both Defiance Bay and Twin Elms. The response to this was... Somewhat mixed, from both the devs and players alike: the players felt Defiance Bay never felt as lively as an Athkatla, and that Twin Elms felt a little scarce in content, and the devs agreed on both cases and likewise felt like their time to come up with in-depth content and proper detail to render such areas was cut short by this division, forcing them to rush the two somewhat. Whilst having four city hubs with an adequate density of content and attention to detail would sound like a dream come true for many, the kind of work required for that would be exorbitant and the likely effect would be one where all four cities underwhelm instead (and as a small gameplay-related quibble here, if many of the quests across these cities would involve doing stuff in other cities, this would also add a lot of backtreading which is usually best avoided in any game, let alone RPGs which tend to be especially notorious for this). In theory one could split a city as dense in content as Athkatla or Neketaka into four smaller cities without losing on the amount of content present in the game, but in practice, psychologically at least the effect seems a lot less appealing.
There's also the matter of what having four big cities means from a setting perspective too - the Deadfire isn't meant to be a place that's very securely settled and has had all these cultures inhabiting it and building settlements on it for centuries, they're literally new to the region, much of which is yet "undiscovered". The settlements are precisely that: settlements. You can see how the majority of Port Maje and Dunnage's buildings seem haphazard and not made with longevity in mind - in the former's case you can even see the state of the wooden planks comprising the walls of the Kraken's Eye for example already rotting away and losing their blue coat of painting. These settlements are *meant* to be small, they're there as an enterprise that even when we arrive to the place the mayor himself is unsure of its present or long-term success. Sayuka is very much a straight military camp. Tikawara has literally built huts out of ship hulls to try and show they're an actual village to those who come and visit them. To make any of these a city would be to dilute the point that all of this conquest, all of this expedition and process of colonization is at a very early stage and happening in the *now*, not decades or even centuries ago. That Neketaka's a massive city as it is has its reasons, but most of all it is because it's the centre of the Deadfire in terms geographical and power-based, it's the capital of the Huana as a culture and the one city presumably preceeding the colonist expeditions and so on. It is, strategically, the only place you'd want to set your base for your expedition (relating somewhat to theories of spatial competition and so on). And, to tie back to what we spoke of before, it also makes for an ideal case study and representation of the cultural clash between all of these factions.
From a narrative perspective the "race to Ukaizo" I believe already does a fair bit of what you propose. Disregarding the incentives from our personal questline, each faction is already given a pretty clear and singular reason to why they want to make it to Ukaizo themselves: the Vailians are interested in what they can learn of animancy in what was once a major Engwithan landmark, the RDC's interested in learning more about the storms to see what can be done about the same in Rauatai, the Huana need it because the history of their people and culture is there, the pirates see it as a place with lots of potential booty and a good alternative to settle in and operate with relative impunity and so on. How we reach there also differs greatly given the choices we make and the faction and subfaction we ally ourselves with: eventually we are made to take part in some kind of move against one of the others and, again, we can see the eventual race pan out in several different ways depending on who we sided with and who we struck against in the process. To remove our attention from Ukaizo would be something that if anything would muddle up the narrative and reduce the stakes making our way there and to confronting Eothas and so on. If anything an issue the game had in its pre-5.0 iteration is that the faction conflict and the threat of Eothas didn't feel connected enough, and that's precisely something this last patch was attempting to address with its narrative additions and so on; so to create an ending that tends further away from the game's climax and thematic crux which is the whole event at the Wheel, I feel would only widen this divide instead. Here's the other thing too: I don't think it's an option to *not* finish at Ukaizo either; the narrative of the entire franchise so far has been built around the conflict of power between gods and kith, and the cultural shift from theocentric to anthropocentric instead. A Rauataian invasion to Neketaka or a Principi attack to Port Maje or Sayuka as expansions or replacements to the current final race to Ukaizo would be fun to play most likely, but would ultimately be rather meaningless spectacle, all in a saga that stands out for being motivated by themes and ideas first and foremost.
Anyhow, some thoughts on my part.