What makes Jigglypuff a great character is her crazy ability to dodge stuff and do fake attacks in midair. When I play as her, I spend most of my time in the air, and try to open my opponent up for attack. Also, when an opponent is off the edge, because she can float really well, it makes for easier edge-guarding than most characters; she can fight your opponent in mid-air, and still make it back in time. It also helps that she has good air attacks.
As for Ganondorf, if you can master L-cancelling, Ganondorf is one hell of a tough adversary to contain. Also, if you know Ganondorf well enough, you can time your attacks just right so that the slower motion of him doesn't really affect your gameplay anymore.
Lastly, throwing isn't as effective as in SSB, but instead it is more of a tactical move. Because you can grab directly out of a shield, if an opponent is coming at you and you block, while they are recovering from their attack, you can easily grab them and perhaps combo them a bit from the throw. Of course, this works in reverse if someone coming at you, instead of attacking grabs you, they'll grab you through your sheild. So really, it's a mindgame at that point.