A lot of what I have to say has already been said in this thread, but there are a couple of things that still bug me.
Alien transporter.
So here's a device which 'faxes' a copy of things (in particular: a person) across space-time. This person can already exist in that timeline, with no ill effects. They are copied in entirety - current memories, consciousness, etc.
The device has a reservoir of 'common element atoms' used to reconstruct the items (person) at the other end. This is explicitly stated as the mechanism by which the device works.
This implies that people are entirely material - they can be reconstructed in entirety using only matter, including the aforementioned memories, consciousness, etc.
If a person had an immaterial 'soul' then the device as described could not possibly copy this. It would seem then that no immaterial souls for people exist.
I suppose it could be argued that the device copies a soul using another mechanism but never describes it. Then why describe exactly how it works, but leave out something so important?
Anyway, going ahead with the conclusion there's no soul due to the material cloning of humans, how does anything else in the entire game series work?
The morphogenetic field concept is probably OK - as a method of sharing ideas between people (an idea pool is not necessary to clone a person, only the ideas they had at that exact moment). A computer can operate without a hard drive of its own as long as data can be pushed into its memory in a way that allows it to operate.
"SHIFTing" would then be replacing a person's current memory with some other identity as 'downloaded' from the morphogenetic field. Why this becomes represented as a physical ball of light beaming down from above into a person's head... who knows?
Edit: But this is only changing the memories/consciousness in the target person. It's not MOVING your current consciousness out of the body and into the target, so shifting as displayed can't really work. I feel like ZTD has just added too many concepts which make the pre-existing ones even less comprehensible, but then people feel like that about 999 to VLR too, so...
It could however be possible to 'force push' ideas into a person to change them, so 'mind hacking' is actually fairly plausible.
There are a few theories about souls and whatnot in the game series which basically become nonsense though. The 'observer soul' somewhere else which is a pointer to a person's body could not be replicated through a person's matter alone. Perhaps the 'soul target' matter could be replicated, but then the 'observer soul' would be pointing at two bodies at the same time, which clearly doesn't happen.
What I definitely have a problem with is Akane's theory of BTTF 'mind swapping' when SHIFTing or whatever. There is no evidence for this shown in-game, and no reason for it to be true (you don't have to take a computer's current memory and place it somewhere else when you overwrite it!). Most of the time the entity being shifted away from is destined to die in an instant, so you wouldn't even be able to confirm it by SHIFTing another person over there to check which 'consciousness' was currently inhabiting them - the one that shifted away, or the one that was the target to be replaced. There are still moral implications with wiping out another person's identity, but it's not quite the same as swapping them into a deathtrap.
Also, why can only one person be replicated in a pod at a time? It can't be a pure mass related problem, because two babies would contain less mass than a full-grown Sigma, for instance. The obvious answer would be that to replicate the consciousness etc requires something which can only be done once in a pod at a time. But they work on pure matter, so why?
On to other things.
The Sigma x Diana ending made me uncomfortable and angry. We're trapped in a bunker knowing we have 10 months only to survive due to lack of food. You go a bit crazy. We discuss your previous physically abusive relationship. You hit me. Later, you get trashed drunk. You ask for sex. I deny it and you call me a coward with no balls. You ask me to kill you. I HIT YOU (clearly she likes physical abuse?). We go off and have sex in an alien transporter pod. You're pregnant, we have no food, I stop eating so you can sustain the pregnancy, because that's a great idea. No food, no escape, time to have babies. The babies happen. We know everything is screwed, so we send them to a RANDOM POINT IN TIME (only stipulation: before Zero obtains the pods) where we have no way of even knowing:
-if the alien transporter at the other end is in human hands
-if it is in human hands, if people monitor it in case babies get transported into them. Babies probably can't open the doors to wander out and say 'hey where am I?'
-if in human hands AND monitored for babies, that the people who monitor the pods will even look after some random babies that get transported into them at all!
Don't even consider sending one parent and one baby so it at least has some chance at the other end!
So now we have two sets of babies, two of which are destined to starve to death right now, and the other two sent off somewhere we have no reason to believe they will not starve to death in an alien transporter pod's output chamber.
What the hell kind of decision making is that? Every decision they made was so stupid I couldn't enjoy that ending at all.
Never mind that Sigma retained super-buff status despite giving all his food to Diana for 9 months.
Argh!
On the plus side, I actually kind of liked the fragment system/memory wiping, because I thought it was a reasonably effective way to combat the knowledge of SHIFTers that came from the future - their current knowledge is being wiped every 90 minutes. I thought this might come up as a plot point, but nope.
Sorry for the rambling. I've got more I need to vent about but can't articulate it right now.