One of my favourite scenes in the original N64 version, just after gefeating Ganondorf the walls and windows start to disintegrate. In the 3DS you just get some 'white snow' effect? The original effect looks much better in motion
http://imageshack.us/a/img560/6784/aq8c.png
Moving on to Ganondorfs transformation, I took these pictures from the following two youtube videos:-
N64
http://www.youtube.com/watch?v=1DMsjR-LE60&feature=player_detailpage#t=2s
3DS
http://www.youtube.com/watch?feature=player_detailpage&v=vX6DbcmC6vY#t=357s
N64 - Ganondorf raises his hand showing that he's 'using' the triforce of power
3DS - This shot has been reframed and it now looks like hes shaking his fist at Link.
http://imageshack.us/a/img854/1368/b2j8.png
N64 - Ganondorf falls back and there is a deliberate blue/white flash surrounding him so that you cant quite see whats happening
3DS - Ganondorf is surrounded by a white mist? You can see everything and there is no mystery.
http://imageshack.us/a/img89/1079/59wp.png
N64 - As the camera pulls out the black outline of Ganon is slowly revealed as the blue/white flash fades away
3DS - Nothing is kept hidden, so there isnt really any suspense
http://imageshack.us/a/img689/9039/3a40.png
N64 - Ganon's full shape is revealed for the first time as two lightening strikes lights up the sky for a split second
3DS - Some dull white flash in the sky, you dont see the lightening strikes and you could already see Ganon before anyway
http://imageshack.us/a/img801/2931/4c52.png
N64 - As the word 'Ganon' appears on screen, his silhouette can be seens against the cloudy sky, he has glowing eyes and shiny gold swords
3DS - You can see everything so the eyes dont stand out, the swords are not shiny
http://imageshack.us/a/img7/7107/zvl8.png
N64 - One of my favourite parts, just after the transformation Ganon raises both swords in the sky as though in anger/frustration at Link, and then starts swinging his swords
3DS - This has been cut out! Ganon just starts wildly swing his swords.
http://imageshack.us/a/img138/8201/enby.png
N64 - Ganon pushes his chest out holding his swords at an angle as though making a 'bring it on' pose
3DS - Ganon just stands there with his arms in the air?
http://imageshack.us/a/img819/2880/uf8n.png