While the indoctrination theory has merits, one thing clearly stands out for me. At the end of the game when Shepard is discussing the control aspect, he says "So The Illusive Man was right after all." To which the child thing says "Yes, but he could never have taken control because we already controlled him." To me, this implies that TIM was indoctrinated and Shepard was not.

Ok, here's what I've summed up from my playthroughs:

1)I don't think he ever sent his Wife to find Jake. He was going to send real Ada after Jake to secure his blood to improve on the C-Virus (something his wife did anyway to use against him.)

2) He made his wife into fake Ada because of some weird fascination/obsession with her. In one of the files it mentions Ada being the only one on his intellectual level, ect, which he admired. He was also pissed when Ada stopped working for him when she found out he was behind the razing of Raccoon City and how dangerous it was to be allied with him. Also, they kinda hint at the idea that they may have been romanticly involved at some point, possibly an affair?

3)I think I covered that in number 2, lol.