You would have to hear the new Ekos/Krystal vs. the old arm/krystal with and without the Keel to make a choice here. Will a Keel and an older, inferior tonearm arm be better than a Ekos with the older sub-chassis? Only you can be sure by listening.
I agree that one's own hearing has to be the judge of any changes made to one's system. However, as every change-and-test sequence will involve dismantling and reassembling the deck - which itself, in theory at least, could have its own effect on sound quality - it is often impracticable to adopt a "change one component at a time" approach. Then, leaving aside the question of what in a tonearm might make it "inferior", there is always the issue of how combinations of components interact.
For instance, in the first incarnation of my LP12 I used the Basik Plus arm and K5 cartridge salvaged from my Basik TT. The performance of that arm and cartridge with the combination of Cirkus, Lingo 4 and Kore was very different (and, in the common opinion of the dozen or so people who listened to it, much improved) over what it had been when mounted on the Basik. How to attribute that change? The LP12 components? The arm showing potential it always had? Both together? I just don't know, though my instinct is that each component, working in conjunction with the others as it was intended to do, contributed to the overall change.
Disregard strict adherences to the "Linn hierarchy." Some upgrades are more passive than others. Arm and cartridges have distinct sound profiles that go above and beyond simply lower noise floors and other benefits of sub-chassis etc. Until those sub-chassis upgrades appeared, you would upgraded the arm no questions asked.
This is throwing the baby out with the bathwater. If you compare LP12s at the different performance levels, as many of us have done, I believe (from my own listening and others' observations) that each level of performance reduces the degree of distinctiveness in the sound quality produced by the LP12 source. In other words the LP12 transcribes the information in the record groove that much more faithfully. Noise reduction is therefore a key element of system performance. You will get reduced, or perhaps no, improvement from changing your arm and cartridge if the mechanical 'foundation' is inadequate, just as you would not construct a luxury house on anything but the most solid footings.
That is not to argue, of course, that improving the arm and/or cartridge is not sometimes the best way to improve a particular deck. And I agree that different component changes offer different degrees of improvement; IMO Lingo 4 to Radikal is a bigger improvement than Kore to Keel, for instance. That said, the degree of improvement from my latest upgrade (Cirkus and Krystal to Karousel and Kandid) has been such that I believe that some synergy is at work, and I am mindful that the Keel provides the all important mechanical connection between the bearing and the arm/cartridge assembly.
The hierarchy, like many other guidelines, is a good servant and a bad master. It is a useful checklist and starting point for deciding which of the available options is likely to provide the most cost-effective improvement. But it is only a starting point. For instance, If I already had the Kore and was making the choice between the Keel and an ex demo Ekos SE, I would unhesitatingly choose the latter. Conversely, if the choice were between the Ekos and and ex demo Radikal, I would probably favour the latter, even if I only had an "inferior" arm.
David