I don't want the companion to just stand around and say "That's impossible!" or "Doctor, what does that mean?" or even just "Eek! A monster!" -- but I do want the companion to be a supporting character and for the Doctor to be moving the plot forward, rather than spending all his time fretting while the companion saves the day. The Doctor should be a lot more cerebral.
I also think the idea of "I am no longer a Dalek, therefore I must be EX-TER-MI-NATED! *kaboom*" should have been more explicit at the end, but that's just me.