Twilight Princess :
+Many iconic dungeons
+lots of new environnements
+Story/characters
+Some really great music
+Great bosses
-The damn controls omgggggggg (played on the Wii)
-The moment you have to save the carriage (yes that does need it's own negative point it was awful)
-Outside of dungeons some environnements were incredibly empty

Skyward Sword :
+One of if not best OST of the franchise
+Great story and characters too
+Great dungeons (but less than TP imo)
+Loved some of the crafting elements
-The 2nd imprisoned
-Lack of environnements
-Overworld was lacking a bit of utility as well
-Feels short

To me, TP feels like the most they could make of the Oot formula. SS was good but clearly the troubles they had during the making are showing in game. The game has only 3 generic environnements and you have to go back for the dungeons which kinda bored me a little. The dungeons were pretty originals tho, music and story were one of the greatest in the series. But still, imo SS also suffers from being the last game of the Oot formula where they wanted to make some changes but couldn't because of the Wii.