Sheesh, as difficult as this is to read I'm not sure why I'm bothering to respond, but here goes.
1. What?
2. You've got a point on that one.
3. Hmm never got that line so I can't be sure.
4. Kreia never wanted the Jedi dead, she only wanted them to see the galaxy and the Force the way the Exile saw it. She wanted them to see the error of their ways and for them to realize she had been right all along. But they weren't as strong as the Exile and couldn't cut themselves from the Force as he/she had, and in the end the pain killed them.
5. Yes, Malachor was important for turning Jedi into Sith. The academy there was not only the source of the assassins hunting the Exile, but Malachor itself was a wound in the Force. Had the planet remained, it's echoes as well as others would have killed the Force and all Force-sensitives.
6. Not sure...
7. They originally offered more to the main plot, but that was cut.
8. The Handmaidens took her. The fact that the Handmaidens were on Dantooine at all is reason to believe they had a ship.
9. Atris and Kriea were anything but chummy. Atris wanted Kriea stopped, and planned to do it herself before the Exile comes along.
10, 11, and 12: The ending is pretty much swiss cheese, there's no point in questioning it. Just know it made a lot of sense before most of it ended up on the cutting room floor. Ask someone else if you want to know all the cut content, I'm tired of typing.