Alright, thank you all for waiting patiently. I'm finally able to sit down and surmise what I believe is the biggest problem with the quincy in this arc.
Even disregarding all the evil assholery and nonsensical schemes, the real issue with the quincy is that they're no longer human. Before this arc, the quincy were defined by the fact that they were human. Sure, they had strong spiritual affinity and had the unique ability to manipulate reishi, but at the end of the day, they were still just human. But then Yhwach shows up with his new hoard of sycophants, and they become increasingly deific. Quincy are no longer regular humans with strong spiritual powers, no. Their progenitor is the "son of the soul king" (whatever that means) and they are the chosen people who will inherit the land. Hell, a handful of them are even over a thousand years old and participated in the original war with the shinigami.
But why? Why go so absurd with the powers and the lore behind them? Much like the hollow allergy, it's really just lip service for the world building. Let's look at that, actually. It was theorized in universe that the reason for quincies total hostility towards hollows has to do with "Primal fear towards something that threatens our lives". I figured being able to see horrible spirit monsters that attack people on sight would be a good enough reason for any hostility towards something. Humans aren't allergic to bears or lions, but we contain a certain level of hostility towards these creatures because they can brutally maul us. If I had the means to eliminate a threat, I'd use them. This only get more egregious when you remember all the times Uryuu was injured by a hollow/arrancar. Yet he still miraculously lives past those encounters. Then there were the times he absorbed Cirucci's spiritual energy into himself and Quilge absorbed that hollow chimera into himself. Neither seemed particularly perturbed in doing this. And of course, there was the bankai stealing. Obviously the heroes were going to reclaim their bankai, but how could they possibly do it? Would they abandon the asauchi and manifest their zanpakuto on their own? Maybe they'll simply break the medal and take them back? Nah, let's give the quincy this weakness that was never a thing before and never mentioned after. That can't possibly be a serious detriment to the story and its worldbuilding.
I want to end this with a 'removed' look at the quincy, so to speak. Looking at Yhwach and the quincy, I honestly think it would have been better to save this kind of stuff for a different faction of antagonists. Keep the quincy human and their grievance with the shinigami purely a revenge one. There's no need to complicate their story with anything. That way, you can have the quincy story and still use the crazy powers/characters at a later time.