The biggest sin is SS because they deserve to go to Hell for it.
Biggest mistake... My knee jerk response is to say the timeline, but I think what I really mean by that is validating continuity at all. A few years ago I cared, I really did. I theorised, I tried to find the connections, I tried to make things fit. But the reality is that they don't, they never have, and they never will. Nintendo don't care about continuity. They love dropping in little references and things for long-time fans, but as far as a linear, cohesive story goes, Zelda has never had that. There are isolated pockets of continuity, sure, like OoT-MM, OoT-WW-PH-ST, or ALttP-ALBW, but these 'continuity bubbles' don't overlap. At least that was true before the official timeline canonised a series-wide continuity.
Now, instead of people discussing connections and trying to fit the games together, we have arguments about whether the timeline is even canon or not, people getting stressed because they don't like it for this reason or that reason, and massive, unignorable contradictions that are now lore. Zelda is a series that doesn't need lore, it doesn't need narrative depth, and it works better to keep each game isolated, story-wise, because that leaves Nintendo the space to do what they want without automatically pissing a large swathe of fans off with contradictions, retcons, or things that can't make sense. Validating continuity implies there are answers to the questions many fans have, when that simply isn't true because Nintendo never gave anything a second thought. They created a wild goose chase with the timeline, and they shouldn't have.
WW said it best:
This is but one of the legends of which the people speak...
They should have canonised that. Instead, they just antagonised their audience.