I invite you to take a second look. The Nation we explore the ruins of throughout Skyward Sword. Ruins in Minish Cap where the Wind tribe are said to have moved from. The entire Hyrule Kingdom in Wind Waker. The sky people connected to the Tower of the Gods in Wind Waker (though this one may be in game or theory; I'm simply going by memory here). The Lokomo from Spirit Tracks. The Eastern Ruins in Link to the Past suggests there was some purpose to the place, and now it's abandoned (This one, to my memory, doesn't even tell us who built the place. It's just an ancient ruin, just because.). The sky islands and the Ooccoo is questionable because the Ooccoo look/behave more like they are squatting in the remains left by someone else, rather than living in homes they built; but more definitivly, that's crumbling too.
I don't know. The people who are said to have helped build Hyrule, possibly the Sheikah, Hyrule itself, the nation that made it possible to forge the Master Sword, and the people who kept an entierly different Demon King (Malladus) at bay? These seem like majorly important groups, to me. Seems like history that important and heavy would leave footprints for more than one game. And, honistly, the people who founded Hyrule would seem to fit in nicely.
The group from Majora's Mask doesn't even have a connection to Hyrule's hystory. They basicilly get a pass because that game is offically self contained. (I say offically because there are theories about Termina being part of other places we visit in other games, but that's an asside.) The Twili are similar, but worse in this aspect, in they are contained in a different realm, but we are only told that there is some great devistating history, that we never see any remains of.
We were able to see that the Zonai were important to Hyrule's history in Breath of the Wild, and it wasn't a one off thing. We got even more in the next game, expanding on the previous game gave us. That's double the game that any of the others gave us to get to know that lost civilization.
But, you've already expressed dislike of the entier trope, that is deeply ingrained within most of the series, of lost civilizations, so I doubt any of that matters. Ultimately, the lost civilization is as important as we are told they are.