I thought the ending, with regard to Brau and Thracia's supercomputer, was fantastic. It had already been made clear previously that Thracia was essentially run by a supercomputer, with the president merely controled as a puppet. From the bears talk in the final chapter and actions in its earlier appearances, it seems quite clear that it is the personification of the computers AI. Though i doubt Braus attack would have been able to destroy it.

Pluto helping Atom at the end was a little cheesy but i've always been a fan of the evil badass turning coat and becoming an antihero, even if only for a few brief moments. The plot to destroy the world seems a little over the top considering the noir murder mystery theme of the rest of the manga, but it was an integral part of the original manga and executed quite well.

Yes, but who created Teddy Bear and Brau1589 (the second one's creator maybe was mentioned but I forgot)? You are saying that Teddy Bear created itself? Then when it says that when Atom woke up all AI's in the world should have been able to feel such a strong AI, it should have been the same for itself, but it almost looked like that noone in the world was aware of it (until the end when imho Atom ordered Brau to kill it).
It's not really clear to me what Teddy Bear is.