Quite a few people saying here (and in some comments along the way through the issues) how no character was pure evil, or it's not nature but how you're raised (nurture)... but that's not what the story told us. In the story we have a pair of twins who essentially had the same set of memories. They were so identical in that respect that for most of the story they did not even know which one of them had been taken to the rose mansion, and in the end it was still unclear which one was unwanted by the mother. In other words, for all intents and purposes they both had a horrific experience at the mansion / with the experiment, and had the uncertainty of a mother that may not have loved them.
And afterwards, both twins had the same opportunities to live in happy households with parents who, presumably, loved them both relatively equally. In other words, they had faced identical "nurture". Also, remember what Franz Bonaparta / Karl Poppe told Anna / Nina, humans can be anything. This goes along with the no-name aspect of things too. These children could be anything and one chose to be "good" (Anna) and one "evil" (Johan).
You also can look at the results of later attempts to replicate the experiment with other groups. Many people wound up committing suicide. Why? Because their nature was not "evil" (or at least evil enough) so they wound up in states of despair.
We might draw a contrast to Dr. Tenma too who, despite experiencing unfair working conditions, injustice in the court system, danger to his life and the lives of people he cares about, and the possibility of losing faith in humanity he still remained (ridiculously) saintly. In fact, it is because of Dr. Tenma's "nature" that other characters maintained or regained their faith in humanity, or hope for the future or the like. That would not be the case if this was all down to "nurture".
Now, that said...
There obviously are a lot of things one can think and talk about based on this story, so it is a fairly strong story, and as far as being a solid mystery / thriller goes, it does that job extremely well. I do feel like it bites off more than it can chew with some of the philosophy / sociology that it plays around with and then never does much with, giving the characters and the audience convenient outs to avoid more troublesome answers.
For one example, Dr. Tenma facing off against Johan at the end, guns drawn. If Dr. Tenma doesn't fire then Johan will kill a child and very well may continue to spread disorder through the world. Johan also won't be punished for his crimes. On the other hand, if Dr. Tenma does fire then it calls into question the whole "all lives are equal" line of thinking, as well as other similar "violence is bad, kay" notions throughout the story. Instead of a tough decision one way or the other, the characters and the audience were given the convenience of a drunk shooting Johan.
It reminds me of a similar cop-out from another Urosawa work that let me down.
There were other missed opportunities too, but I will leave it at that, at least for now. Still, I'll give this a 9/10 (or at least a strong enough 8 that I am willing to round up).