Oh man. Yeah, I remember feeling ahead of Stormblood that they were focusing too much on trying to make pretty UI elements for each job without really considering if they were necessary or complementary to each Job's feel.

WHM's Lillies are a great example, but so is SCH's Faerie Gauge, notorious for its sole use being "Fey Union," then and again now that they've removed Fey Blessing from it. Fey Union itself has always been stupid, IMO. Too many buttons to push to get what amounts to what Rouse already did anyways, and they very specifically had to nerf Embrace entering StB just so that Fey Union felt like it contributed something worthwhile. The Aetherflow's UI element is probably more useful because it's more central to how the job operates (I think it should also display Aetherflow's cooldown visually, and this would have made even more sense during StB when Aethergauge usage reduced Aetherflow's cooldown).

I think the best example of the Faerie Gauge being an engaging system was during ShB PVP, actually, when you would generate gauge via healing/damage spells at a rate of 10/20, and then you could convert 50 gauge into a Lustrate charge and a short 150% damage/healing buff. It was a simple, fun and impactful to the game plan of SCH, and it had the added benefit of high risk-high reward where if you played offensively you could be rewarded with more damage and free heals, where if you solely healed you would much more slowly accrue resources and wouldn't be able to maintain the buff for most of the time.

At least Lillies and Faerie Gauge could mostly be ignored. In the worst cases, they completely altered certain jobs to fit their system. MCH was pretty significantly changed so that the heat gauge could be a thing and you had almost control over it until max level (Flamethrower is a vestige of this). BRD was well received, at least. DRK was changed pretty hugely too, but that probably has more to do with the changing cross class to the role action system at the same time.

The job gauges were often a case of systems outside of job design or the battle system arbitrarily affecting job design, rather than for an actual issue that needed addressing.