Actually from what I've read, Skyward Sword's plot was created after technical development had already begun, and that's pretty much standard procedure for Nintendo. That's not a bad thing either, as from what we're hearing, the game's story is smashing. I do agree that Nintendo has a general idea of what they're going to do in the future, and that they'll even handle the placement and plot of their future games with more gravity in regards to its placement within the timeline; but that's all forward motion. Retroactively, I seriously doubt they're spending or have spent (comparatively to fan-theorization) much time studying where it would be best to place their older games.
I've worked on tv shows, and video games with a lot more plot than the Zelda games have, and I've borne witness to meetings in those contracts in which connecting plot-lines are discussed. You'd be amused and staggered at how easily even the head writers forget and lose track of the details of what they've created. Again, don't think I'm trying to detract from the Zelda process. They have their methods, and it keeps me coming back over and over; so they must be doing something right.