A few months ago I saw a thread on whether or not Trolls belong in Shadowrun, and the conclusion I saw was that the majority think they do. That something has to make Street Samurai afraid of going to prison was my favorite argument.
I have the same question about cyborgs. Here is my take:
1. The Essence problem. Based on the Essence loss from other types of cyberware, I would think a brain in a jar would have an Essence far lower that 0.1. If you are just a brain in a jar, the astral self no longer recognizes the physical self and departs, and then without it the brain dies.
2. The targeting problem. From Augmentation "Mana spells are simply unable to lock on to the the cyborg's living component and are useless as a result." Couldn't the same thing be said of Full Body Armor? The explanation given is that there is a double inanimate barrier: {cyborg body}->{CCU}->{living brain} instead of just {full body armor}->{meat body}, but something like full-body FFBA under Full Body Armor could also have the correct properties to prevent targeting of Mana spells.
An obvious solution - make it like a Cyberzombie. A Cyberzombie is basically a soul bound to an artificially sustained corpse.
So for a cyborg, maybe be explicit that the astral self is locked in that CCU as well. Maybe the special sauce in the MCT surgical procedure is a layer of Orichalium in the CCU and the SR equivalent of the Magic Jar spell (haha).
In any case, if cyborgs are going to be in Shadowrun, let's make sure they make sense.
Edited to add SR4 tag.