Why did Chise allow those bombers to reach Sapporo in the beginning of the series? She could have easily intercepted them before they even reached Japan's coast, and you'd think that the conventional forces would have sent fighter planes, or would have tried shooting them down with ground-to-air missiles. It is unlikely that those slow airplanes would have managed to drop even one bomb on the city in the case of a coordinated counter-attack.
That's a good question. For as far as I've seen, every time she faces the enemy, she blows up a city. Kind of kill the whole purpose of defending in the case of Japan, and attacking in the case of its enemies. Why not just nuke everything, you'd get the same effect with less casualties? I guess the series isn't about realism as much as drama.