A few comments if we are "brains in vats":
1) Some things cannot be reduced to mere simulation. Self-evident principles would still be self-evident. And we would still be certain of everything reducible to self-evident principles. Thus, theism, for example, is untouched.
2) Christianity and all religions would just be a simulation (by definition).
3) I am convinced that free choice is self-evident. And, that there is something about free choice and consciousness and the operation of the intellect that cannot be reduced to purely material causes. Thus, on my reckoning, absolute determinism and materialism are false. Thus, if I am a brain in a vat, I am not merely a brain in a vat.
4) We already have a good analogy to this brain-in-a-vat situation that we all experience: dreaming/hallucination. It is possible to experience a dream and think it is real. So it doesn't seem possible to a priori exclude the possibility of some aspects of our wakeful state itself being something like sleep compared to...I don't know...some higher state of consciousness that we haven't awoken to?
5) Regarding #4, I think we find something like this already expressed in Christian Theology? That this life is like a dream/sleep compared with the afterlife? That the next life is more real? In our "childhood" we live in make-believe but then we grow up? "For we know in part, and we prophesy in part. But when that which is perfect is come, that which is in part shall be done away. When I was a child, I spoke as a child, I understood as a child, I thought as a child. But, when I became a man, I put away the things of a child. We see now through a glass in a dark manner; but then face to face. Now I know in part; but then I shall know even as I am known" (1 Corin. 13:9-12).
6) If, per #1, theism could still be proven true, then perhaps one could argue that God, being Truth Itself, could not allow such a thorough deception of being brains in vats? Just food for thought...
7) If we are indeed brains in vats, then our actions in the simulation have no more moral significance than our actions in a video game. But, it seems that the most that can be said is that "brain-in-vat" is a hypothetical possibility, not that it is a certainty. If so, then I would argue that morality (considered subjectively at least) remains unchanged. If one is uncertain whether "reality" is real, then one should err on the safe side. Thus, unless one is certain that we are brains in vats, it would be immoral to act as if we are so.