The Master Sword was actually one of the things I was thinking of: ALTTP claims that it was created in response to Ganondorf gaining the Triforce, but that it was unable to be used for want of a worthy wielder. Ocarina shows the opposite on both counts: it predates Ganondorf (by a lot) and it WAS used against him. (...Or at least, the English-language manual claims that. I think that's not considered canon these days; but even if that's true, if Nintendo cared about canon they wouldn't have shipped a non-canon storybook with every copy of their game ).
Ocarina also ends with the Triforce in three pieces, and with Link and Zelda (and Ganondorf) each having a piece; ALTTP shows the Triforce whole and in Ganon's possession. Also, the sages in Ocarina are mostly non-human, while their descendants in ALTTP are human. A war between the Knights and Ganondorf's forces probably happened during the time skip in Ocarina, but the sages weren't around yet and it had a different outcome than the one described in ALTTP.
I'm not really sure what my point is, since I also wish Nintendo would do better with continuity in the Zelda series, and I also think Skyward Sword was a mess. It's just... it really has always been this way.
(Ironically, I think Skyward Sword is such a mess in large part BECAUSE they decided to give more focus to the lore. They ended up proving how little they knew or cared. I like to say that Skyward Sword committed the cardinal sins of both story-focused games and lore-focus games: They tried to make a story-focused game without focusing on the story (and on making it good), and they tried to make a lore-focused game without studying the lore. In the end, though, I think that the game's main problem on that front is bad writing, and that a sufficiently good writer could have salvaged their somewhat ham-handed lore additions. I think it also really suffers from having the wrong main character. The story they wrote is about Zelda, Impa, Hylia, and Demise; but the camera stays glued to Link. Even while Groose is around, which is really just an extension of the same problem, but deserves special mention since the game would be, like, 20% better if they just cut away to a nice field of wildflowers or something whenever Groose was around.)
(D_E has almost completely purged Ghirahim from memory)
I was thinking about the original Star Fox vs. Star Fox 64, and also Star Fox 2 vs. the original Star Fox. That might well be unfair, since 64 is clearly a remake of 1 and 2 was never released, but does go to my point about how they were just re-using the same plot over and over again.
The overall impression I have of Miyamoto is that he'd happily make iterations of the same few games over and over again. I think he's on record as being against having an overall timeline connecting the various Zelda games, ie, I think he always considered them variations on the same story, rather than parts of a larger story.
I think the main evidence was that the previous Earth Sage was a Zora, and that Medli was stated to be a descendant of hers.Yes, I would say this is an unintentional positive. I always thought the evidence that the Rito were descended from the Zora was very flimsy. It's based almost entirely around the fact that a symbol is present in both cultures, a symbol that the Rito could have simply just found in some ruins and liked the way it looked and so adopted it.