A lot of people hated on this series, especially the older episodes. I, on the other hand, love them all. I watched 1&2 shortly 2 was first published and I followed the series since. I was so excited when eight came out, and boy, the wait for nine was intense. But, it was worth it. Unlike a lot of people on Newgrounds, I actually like the art design. Link should be a musclebound badass instead of the pretty boy elf Nintendo made him. I really wish the combat in the official games mirrored this style, but then I suppose other Zelda fans would freak out that it's not puzzle based and not call it a true Zelda game.*
As far as Ganon laying his hand on the sword that banishes evil, he had taken on his true form at that point, and had darkness sufficient to overpower the blessing of the goddesses. If that's not good enough of an explanation, then I don't know what to tell you. MInd you, this is just speculation, though. I could be wrong, but it's my guess.
*Oh yeah, there was that one Zelda-themed Dynasty Warriors game. Huh. Wonder what that's like (I don't own a Wii, so I guess I'll never know.)