I think, just as you said, the book's very title is a reference to Caliban, suggesting that he should be central to the story. I agree. Caliban in the context of colonialism represents the undesired member of that society - much the same as prisoners in today's society.
In the Tempest, Caliban is taught English and his feedback to it, in the quote:
Warning: spoilers follow!
The first person to ask Jimmy to take care of the Crakers was Oryx, on the last night of her life:
“Jimmy, I want you to promise me something.”
“If Crake isn’t here, if he goes away somewhere, and if I’m not here either, I want you to take care of the Crakers.”
“Not here? Why wouldn’t you be here?” Anxiety ...
The mother is "dwindling", receding from life, but still stubbornly living on.
This is clear from the first stanza of the poem:
My mother dwindles and dwindles
and lives and lives.
Her strong heart drives her
as heedless as an engine
through one night after another.
Everyone says, This can’t go on,
but it does.
It’s like watching someone drown.