The ruins shown in the lightning scene appear to be Castle Town and it's fountain, comparing the scene to the one of Castle Town being destroyed. The flags are still there, very similar to the Twilight Princess Castle Town and fountain I might add. I also noticed that Zora girl Mifa has the Zora spiritual stone symbol as part of her attire.
Just noticed in the scene with the fallen Sheika defector where Link is Defending Zelda... the Master Sword is in pristine condition. In fact the sword is in great condition throughout. Its only shown ruined in the beginning scene, which contrasted with the scene at the end of the video, makes me think we will be restoring the Master Sword in the game. But who knows?