It's a tough choice. I always liked the backstory of WW, how without Link, the Goddesses had no choice but to flood the land that they watch over.
However, Majora's Mask was such an amazing game with such a great narrative, so I can't really chose which side I prefer.

Twilight Princess started out great, but as soon as Ganondorf was introduced, the story was killed. So that really brought it down for me.

As for the actual timeline, I'm not really sure nowadays. I used to believe whole-heartedly in an AT timeline, but now I'm not so sure.