This is probably out of topic, but Skyward Sword's Master Sword would be new, considering it's the first time anyone has ever used the Master Sword.My favourite would have to the Skyward Sword Master Sword. It's because I've seen the Master Sword evolve so much that the newest, cleanest version is just more visually appealing to me. HOWEVER, I still think the one from OoT is more epic, because the first time you step inside of the Sword's chamber you're just like: Wow.
WW only has to be re-powered up with prayers. Going by a general timeline, ALLP's has the light sols, a refining from a blacksmith, and the power of a Great Fairy! That's quite a bit more power than OOT or SS.Now that you mention that, it brings the thought that ALTTP's (and subsequently TWW's) Master Sword is stronger than OOT's, TP's and SS's Master Swords, as it was upgraded and made more powerful than it was originally.
Yeah TP really gets a bad rep as a Zelda game. Everyone goes like "oh, TP is too easy; TP is nothing compared to OoT", but it really is a good game. The environments are huge, the character models are basically perfect (I like TP Link and Zelda over SS), the weapons are cool, and the dungeon are very distinct and well detailed.