One has to wonder what a brain operation inside the Matrix entailed from the patient, since there is only a plug into the back of the neck, and not the machines opening up pods and doing actual brain surgery. — Marchesk

Well, the simulated brain could be kept in sync with the vatted one, which works most of the time. An aneurysm in the vat could be reflected in the body, but there are certain scenarios like the effects of high G forces that would make an accelerating brain behave (black out) very differently that the one in the vat. Concussion comes to mind. That is not just fake experience that can be fed to the organ in the vat.

Matrix movie, like all entertainment, is not science. It is founded upon unrealistic premises and works only because the writers make it so. For instance, one purpose of envatting people was to harvest their heat and electrical energy. Guess what... People consume energy, they don't generate it. Far more efficient to just burn whatever they're using to keep the bodies alive.

Guess what... People consume energy, they don't generate it. Far more efficient to just burn whatever they're using to keep the bodies alive. — noAxioms

Yes, that was dumb. Originally, the premise was that the machines were using human brains for processing, but it got changed to something more easily understandable by audiences.

It would have been better to have the machines doing it for our own good, which falls in line with what Agent Smith says in the first movie to Morpehus, and what the Architect tells Neo in the second movie. Also from the Animatrrix stories, we find out that humans started the conflict, so it would make sense for machines, upon winning, to put us in vats and find a use for us.