The development conversation was interesting, about how the Zonai's background had to change because the gameplay was shifting
The Zonai were originally intended to be a highly magical culture with no technology. The device system was intended to be a magic system, with the battery as the magic meter. But the design of the various components became more and more analogs for technological things so that players could understand them, which lead to changing Zonai history.
I don't think it changed the history so much as it looks more technological than originally intended. It's still magic.
Anyway, I like both, but I think I'd give the nod to the Zonai. The Sheikah have the benefit of having been established for a much longer time, we've obviously been waiting much longer to learn more about them than the Zonai, and I think the Sheikah from Breath of the Wild actually do seem like a more natural progression of the ones from previous games than it may seem at first glance. Before BotW fans focused a lot on the ninja aspect because that's cool, but the idea of them as engineers/researchers/an intellectual class in general was actually present from the beginning too. Gossip Stones are like a more primitive form of Guidance Stones and the Sheikah Slate, being able to take in information and parse it for human consumption, Robbie was even able to give one more of a personality much the same way the Gossip Stones are a little more informal. The Shadow Temple is lit with blue flame throughout much of the dungeon, and is the most "industrial"-looking of all the Ocarina of Time dungeons, with rivets, wheels, pullies, chains, etc. throughout, whereas a lot of the other dungeons in the game just have the more "inexplicable floating platform" type of machinery that doesn't even seem like technology a lot of the time. Characters like the Composer Brothers, who seem to be Sheikah since they were born in Kakariko instead of moving there when Impa opened the village, are trying to scientifically analyze the mystical powers of the Royal Family. They're also more generally the lore keepers of Hyrule, with knowledge of the Master Sword and Triforce.
But even though I've just been giving props to the Sheikah's portrayal in Breath of the Wild, I still think the Zonai are a little more interesting. The primary reason for this is the fact that the lore surrounding them isn't as laser-focused (pun intended) as the Sheikah lore is. In Breath of the Wild, we're told the Sheikah had brought Hyrulean society to the point where monster attacks weren't a problem, but other than that everything we learn about them is based around opposing the Calamity. We almost never stumble upon Sheikah ruins that seem to have some other purpose, every shrine, divine beast, and tower was put there expressly for the purpose of fighting the Great Calamity when it happened or to train Champions to fight the Calamity. Some of the details surrounding that are pretty cool, I love the sokushinbutsu references and the idea that they received a divine revelation to do this stuff, it plays into the theme of service and devotion that the Sheikah are often connected with in a cool way, but it still feels less like relics of a whole civilization and more about things designed for one purpose. The one exception to that is the Sanctum in Hyrule Castle having a Sheikah astral observatory beneath it, which is a really cool bit of environmental storytelling, but it's the only glimpse into their overall society I can think of.
On the other hand, with the Zonai it feels more like we're excavating pieces of the society as a whole, of Hyrule at it's founding and the Zonai and Hylian tribes which predate it, and we're still not getting the whole picture but we're getting a lot of tantalizing glimpses of different facets of them. We find structures with different uses in all three layers of Hyrule, some spiritual and some practical, some of the Zonai devices have lore attached to them explaining what they were used for in ancient times, each tribe of Hyrule seems to have had a different connection to the ancient Zonai and Hylians, and even the remnants of the Imprisoning War aren't all uniform, they reflect different perspectives on the same era. There's more of a suggestion of a full picture, but also more mystery, attached to the ancient Zonai/Hyrulean relics in comparison to that of the Sheikah in Breath of the Wild. Plus, I think those who are calling it a retcon are massively exaggerating. If anything, they managed to synthesize a number of things from previous games into something that feels more cohesive than ever.
