The Children's plan included destroying or disabling all Evas because, in spite of all talk about an unified world order being a good thing, they realized leaving a bunch of superpowerful giant robots in UN's hands was NOT a good idea.
Asuka did not like Kurumi, not even after she saved Shinji's life. Her attitude might come across as mere, unreasonable jealousy... until you realize Kurumi got Shinji drunk and slept with him. In other words, not only Kurumi raped Shinji but also she is not even aware that it was rape. Of course Asuka dislikes her.
In twelve years SEELE had time enough to build nine new MP-Evas, not counting all models and prototypes sabotaged and blown up... but HERZ barely had time to rebuild Unit 02 and build a new Unit 00?
In this story the UN is a world government de facto. And they keep under their control a bunch of weapons of mass destruction, impervious to conventional weaponry, to unleash upon whoever inconveniences them. Think about it.
