I think TP is better. SS is a great game, but I prefer TP.
There was much more to do in TP than in SS; there were a lot of chests, grottos, caves, etc. scattered around Hyrule. In SS, there weren't much of these things. SS was very easy to complete IMO, I had everything before going to the final fight with Ghirahim, and I barely used a guide. In TP, it took me a lot of time to get all the things I hadn't gotten before, these include Pieces of Heart, Poes, and some chests around Hyrule (which I'm still not sure if I have them all). Even though using the Wii-motion plus was pretty cool, I still prefer combat in TP; I think those hidden skills were very cool. SS's dungeons were very short, but they were all very cool, and Sky Keep was one of the best dungeons in the series IMO. TP had more dungeons. I think turning into a wolf is pretty awesome.
Flying with the Loftwing was pretty cool, but there wasn't much you could do with it; with Epona you could go all around Hyrule shooting enemies with your bow, which was epic. The Silent Realms, and the Twilight Realms have the same concept, but the Silent Realms are better (but they're scary as heck). Midna is way better than Fi.
And that's all I have to say.