Personally, I don't think that Skyward Sword will make a giant impact on the Zelda series. It seems that every time we get a new Zelda game, we are always discussing about how it will make such a giant impact on the series as a whole, but usually they don't. I'm not saying that Skyward Sword won't make any impact on the series - most games do in some way or another - but I am saying that it won't change anything big that we'll see down the line for many games to come.
Skyward Sword, with the implementation of Wii Motion Plus, will undoubtedly introduce many features that haven't been seen before in the series. I have a feeling, though, that we will only get one other game after Skyward Sword until the release of the Wii 2, which, as quoted, will "surprise people". There is really little that new games can impact on the series as a whole. We get a new console every few Zelda games, and we get games on the portable systems and others at the same time. We get maybe 3-5 games every generation that we see now. We get a 2 or 3 on a handheld, and 2 otherwise. By the time they start to make the third game, it will be a new generation. Since gameplay changes dramatically with each change in console generation, there is little that can make a huge impact from previous games. A lot of what's in the games is gameplay-related, and can't be simply converted all the time from one game to the next. Something big, like storylines or something like that, also can't have too big of an impact on future games seeing as how each game's story is rather unique and we don't want to see reused ideas from an old story.
I think the best thing that happens to the series as it develops is the new things that we are given, and I personally don't care how much Skyward Sword or any other game affects the series as a whole because I want to see something new. If something was an absolutely huge hit from an old game, that's fine. It can be used again, as long as it's not an exact replica of something that we've seen before so it bothers and bores us. I want to see new things so I can get excited and try out different things that I haven't done before. It's preferable that a game doesn't impact later games in the series. This is to an extent, of course.