Well, I correctly predicted the original motive, that this was all planned by Shiki as an elaborate 15-year long conspiracy to commit suicide, with her daughter carrying out the actul killing, but not the result. That it just "didn't go according to plan" is a bit of cheap misdirection. I kind of feel like the writers cheated a bit on a few things just for the sake of throwing the audience off.
The helicopter scene when Miki/Shiki arrives at the lab, it is after sunset, the heli is idling and the director is clearly alive. Did she board the heli seconds before everyone arrived at the roof? Does he have a knife sticking out of the back of his neck as he gives the thumbs-up? In this episode the sun hasn't yet set, we see her greet the director as if seeing each other for the first time, and are shown her stabbing him as they embrace.
When Moe has a conversation with Michiru in the isolation tank the first time, static aside, she looks identical to the image of Dr. Magata that appears on screen. Saikawa even says “it wasn’t Dr. Magata that you saw." At first I thought that this meant that Shiki's daughter had been uploaded, since it happens after the suicide/murder. She even implies it:
[Michiru]: "Nishinosono-san, in this place, you can see the things you want to know right away. The people you want to talk to are always in front of you. The original world was like this. The world you live in is a very restrictive place. Even if you are given a lot of information, it is all quickly forgotten and lost. But it isn't really supposse to be that way. Nishinosono-san, will you come to this side? What's wrong? It isn't scary. This was how the world was suppossed to be."
It would appear, though, that it was Magata using her daughter's appearance. Allowing the character to appear in any form through the VR interaction is deliberate subterfuge.
Shiki's daughter's demeanor during the interview with Moe did not suggest she was lying when she was asked about "her" experiences. No matter how well trained she was by Shiki, pulling that off in such a natural way is a bit of a stretch.
Some final thoughts: I think it's significant that the doll/Magata Michiru (as one of Shiki's personas), the robot, and the persona that Moe spoke to in the isolation tank are all identified as Michuru. Each of Shiki's personalities were created following the death of someone close to her - Kurimoto Kishio, her twin brother who died shortly after birth, Sasaki Suma, based on Morikawa Suma, the maid who died when she was in America, and Magata Michiru, "the name of the doll that she brought here, when she came to this lab" (according to the director's wife) who was apparently created at the time of her parent's death. Magata Michiru is the only one who doesn't fit the pattern of a personality created after the death of someone close to Shiki. The idea that Michiru is "the doll that Shiki brought with her to the lab" came from the director's wife, who clearly has some issues with facing reality. I think Michiru IS her daughter, and was never one of Shiki's personalities to start with? Since her daughter's death, she may actually have become one now, as evidenced by the conversation with Moe in the isolation tank (assuming it was Shiki, and not an uploaded version of Michiru). I would really prefer it if Michiru was able to live on as a ghost in the machine, rather than as just another one of Shiki's personalities.