I think that the Angel they have now isn't the original one that was there at the start of The Angel Experiment. When she was kidnapped, Itex/The School replaced her with an enhanced clone specifically designed to undermine Max and destroy the Flock from within.
Now, let's go with the theory that Jeb was a good guy at heart, just using very, very bad methods to accomplish his ends. He knew about the By Half Plan, he wanted to stop it - so he engineered Max with the specific purpose of destroying Itex from within, and designed the rest of the Flock to help her. (Note that each of them has a specific skill designed to aid her efforts to save the world. Fang is the writer and communicates their cause to the outside world, Nudge is the hacker, Iggy the explosives expert, Gazzy can create trick voices to deceive villains and Angel can read minds. And, yes, I'm going by their powers in the first few books, not the mutations in book 4 on.)
Someone at Itex got wind of this, and decided to undermine Jeb's plan to destroy Itex from within by destroying the Flock. They knew killing them outright may not be easy, so they decided to destroy them gradually from within by undermining Max's leadership. And so, to accomplish this end, they kidnapped Angel and created Angel-2 from her. When Max woke up in the crate at the School, the Angel next to her was the clone.
The original Angel was still kept at the School. In fact, when they saw the clones marching in the yard in Germany, the alleged "Angel-2" could have been the real, original Angel, which explains why Angel said "Uh-oh!" when she saw her. And Angel-2 used a combination of her mind control powers and the Flock's own emotions to manipulate them into throwing Max out.
As for her flash of humanity when Fang supposedly died, it could be that Angel-2 carries some of the memories of the original Angel, and seeing Fang like that awakened those. Or, maybe, the moment simply made her realize her actions could have consequences.
If this is the case, the series could very well come full-circle, with the very last book involving the rescue of the real Angel, plus an all-or-nothing showdown between Max and Angel-2.
An alternative to the flat-out clone theory is that Angel's brain was tampered with when she was at the School, to the same effect. In any case, it's still not the "real" Angel anymore, at least personality-wise.
Opinions? Other theories?