they could still go back to the manga story, just have to change a few minor details, such as when rukia comes back and stuff like that. The fact that he (Ichigo) has trouble going into Bankai allows to follow into the issues he has later in the manga aswell.
I do agree though, the prodiucers, or rather directors are pretty sucky at comming up with original stories and keeping the world and laws of bleach intact :/
For one, how the hell was that water bound kid able to have his water doll go inside Ichigo's body and do damage form the inside when technically his body was still laying limp at his house where he left it?