I don't really know if I have enough knowledge of the game to comment on is Skyward Sword will be better than Twilight Princess. Firstly, I'd like to say that as far as I know, I am one of the few members that I can think of that actually like Twilight Princess. Many members seem to give Twilight Princess undeserved hate because they either just say "It was teh suckage" without any explanation as to why they believe that Twilight Princess is a bad game, or they got too involved with the hype, thus, being greatly disappointed.
I'll have to admit, the use of motion sensing in Skyward Sword has already made me decide that the control scheme for this game will be by far superior to that of Twilight Princess. Twilight Princess didn't really capitalise on the motion sensing controls outside of using the Slingshot, Bow and Clawshots, it was just swinging your arm constantly, which after a while can get rather annoying to do. It lets us have more control over Link when we are fighting any enemies we come across due to the fact that we can move the sword in practically any direction we wish, something which I think is a rather good idea to have included in the game (although the E3 showing wasn't exactly helping Skyward Sword's cause with this, as most people know the motion sensing didn't really work to well).
Another fact that has made me think that some aspects of Skyward Sword will be better than Twilight Princess's is the fact that the enemies, to a certain degree, have started to use better defense mechanism's, in terms of the Deku Baba's, or have learnt to defend themselves with their weapons, such as the Bokoblins. It annoys me that in most Zelda games, there are only two or three enemies that have the items/tech or brains to actually defend themselves. The Darknut's, Dodongo's and Staflos all could defend themselves to a slight degree in Twilight Princess, but once you worked it out after about 2 or 3 attempts attacks, that enemy never really bothered you again (although using my counter strategy to beat the 3 that clustered together in the Cave of Ordeals to forever since they wouldn't split up. D=<).
An the other hand, I personally think that Twilight Princess has the better graphics of the two. If Skyward Sword had Toon Link in it (or Wind Waker Link, which ever you prefer), then perfect, I'd be extremely happy with the game. However, it does not to my dissatisfaction, it has a Twilight Princess Link in Cel-Shading, something that in my opinion, does not go together well at all. Although, this isn't much of a problem because I can't tolerate bad graphics, but it does annoy me.
Outside of that, I don't think there is really much to compare because out of the possible bosses and confirmed items that I have seen in the E3 showing of the game and the trailer that has been released recently, I think that both Skyward Sword and Twilight Princess have great ideas in both sections. So really, I can't quite tell if Skyward Sword will be better than Twilight Princess. Although I can state that I think that it will at least be on par, which from my point of view is something, considering I see Twilight Princess as one of the best games I have played.