One of the Zelda team guys that was interviewed during E3 stated that the events of Skyward Sword lead up to OoT. Now this doesn't mean they can't put games in between these two (they can do or change anything if they feel like it), but it does seem to suggest that this game won't be close to 1000 years before OoT, more likely around 100 or so. It also seems to suggest that OoT could be thought of as a direct sequel to SS, which would mean that the ending of SS will setup the beginning of OoT.
He may not have meant it in this way, but that is what I got out of it.
The problem with it being 100 years is that 100 years isn't ancient. The Master Sword became the Master Sword in ancient times, as the Temple of Time was built to house it, and it was made in ancient times. Plus, the Master Sword is legendary. Things don't become legend over 100 years. Just sayin'.