I think it depends on which kind of song she is singing. Recently she has been doing a lot of rock-songs lately and maybe she has been ''forced'' to use a different technique than what she's been used to...
If you pay atention in MW you can hear that the ''nee boku wa no''-part after the second chorus is much better than the verses and etc. She isn't strainging her voice as in the faster parts where she has to be fast with the lyrics, sing with a lot of power and hit the right notes. And like someone said earlier, MW doesn't really have a clear melody.
To sing a full on rock-song you need a really powerful voice. I'm not saying that Ayu doesn't have a powerful voice, it's just that it's not enough. That's why she's strainging it so much
I simply guess that her voice isnt really suited for rock-songs. I hope she'll go back to pop or ballads from her My Story- m(u)- Secret- era
I belive that was when here voice was at it's best
So keep it simple, Ayu