I personally have a hard time choosing between the two, they both have very attracting parts.
In the gameplay part of things, they excelled in very different ways. SotN did have better level design, there's no question there, and the wholesome castle really had a good progression going on. The Inverted Castle is also something I actually liked, unlike most people. It had a good feel to it, and the level design actually made a lot of sense. While some places seemed a bit less solid than in the normal castle, some places were designed very well, providing even more interesting places than in the normal castle.
On the other hand, OoE excelled at every other gameplay aspect: It was smoother, with a better battle system, improved back-dash and the ground-slide (although the latter two were fixed before OoE, but...); it had better enemy placement, as well as overall better enemies, making for much more of an actual challenge, as well as making it much more fast-paced; and then it had much better bosses, some of the best I've seen in the whole series. And with DoS in the series, that's saying a lot!
So I guess that in this sense OoE is better.
But then there's the aesthetics. SotN is better in this regard, with both better graphics and better music. Even though OoE has very good visuals and music, it just doesn't deliver the same amazing experience that SotN does.
So, I've only played OoE once and I haven't played SotN for a while, but while OoE may deliver much, much, MUCH better combat and more fast-paced gameplay, SotN somehow manages to give a more fulfilling experience. And the levels are also designed better.