Not quite as critical as the Doctor, deciding on who this Doctor's companions are can be interesting.

Anyone who has any ideas, feel free to speak up.

But, here are some ideas I had for Companions:

Sally Sparrow
Jenny (the Doctor's Daughter; if she doesn't become the Doctor in the game)
Doctor Mysterio
Lady Christina de Souza
River Song (resurrected after the Silence in the Library)
a 'good' Dalek