The story about Onan is about the birthright, and responsibilities of birthright sons. The first son of the first wife inherited the birthright and would inherit the majority of the family's wealth, as well as the responsibility to provide for his mother, unmarried sisters, widowed sisters-in-law, etc. Especially concerning the house of Israel, the birthright was particularly sacred and important. In that line, the birthright son was responsible for keeping the sacred writings (what would become scripture). That meant re-copying what was already written so that the writings would not become lost with time since the writing materials they had were subject to rotting and fading, etc. They were also to keep the record current by adding their own writings. These guys were pretty much expected to be prophets and leaders. Even more important, the birthright of the house of Israel was the line through which Jesus was to be born.

So, in that line of inheritance, God was somewhat selective. He didn't want someone in that position who would blow off his obligations or be wicked or wilfully disobedient or selfish (Onan did marry his dead brother's wife, and apparently wanted the perks but was resentful and refused to sire children, which was the whole point, when one of those children would get the birthright, leaving Onan out of it). This was not the kind of person God wanted in that position. Also, it was important to have someone to inherit the birthright (it eventually went to the first son of the second wife, Joseph, since Judah did not produce a worthy heir).

Cain had a very different role to play in God's plans for the world. Besides, doesn't God have the ultimate say on how long any of us live in this world? I might not be remembering everything 100% accurately, but I don't think that the Bible details how Onan and his brother were killed. Maybe when it says that God slew them, it means that they got sick or died in their sleep. I'm not sure on that point though.