I disagree about a couple points, but you bring up some pretty good things.
The Kokori village is too long, and yeah, DEFINITELY is just a big repeat of the structure of the Deku village. However, we can convey a lot of the world's lore in this area, and it would be a shame to miss out on that.
What I'm thinking now is that we should make most of the quests here optional. If you walk into the area, most people will recognize it as a ruined, overgrown Kokori village, because we've all played OoT. That will be enough to get the point across of hey, the Kokori were here but died off.
But it'd be really cool to still have more detail, like, during his quest for the triforce before, Ganon uprooted the Deku tree. Then monsters started moving in on the area, and the Kokori died off, etc.
The main points for the current-day plot of KoT, however, are given through the interaction between the Hero's Shade and Maple. So why don't we have it so when Link walks into the area, he sees them, and then can proceed directly into the temple after Maple. If the player wants to, they can check the village ruins out and find some journal pages giving details, solve a puzzle to find the Kokori sword which might be a trading quest item, etc.