Well - Let's see...
Preganancy is a natural consequence of sex without protection or birth control. In three instances, the MC thought he was playing with someone who had birth control, though he was never smart enough to ask. In Amy's case, she told him to stay inside when he was about to cum. She was actually ignoring his warning that he was about to cum because she wanted to cum herself. Anyone who does not seriously consider the possibility of pregnancy is an idiot.
A story that is always changing while the game is being developed. Isn't that the very definition of a game under development? The quests for Sandra, Daisy, and Beth were not changed; they were finished. The remaining content was added after the point where their stories stopped in the previous versions. Without the video of Tom and Beth's mother, the MC could not have blackmailed Tom into accepting his plan to free Beth's mom for Tom thereby freeing Beth for the MC. In story-telling, we call that a critical plot point. Now that their stories have been completed, they make perfect sense; Sandra's drug debt, Daisy's popularity and daddy issues, and Beth's miserable taste in boyfriends and mothers.
BoN's got a nice handle on the stories themselves. Rewriting Maria's initial quests helps better define how she comes to be seduced and her deteriorating relationship with his father. The teachers quests gives going to school a more solid game purpose. He's expanding a single-thread story into a main trunk story surrounded by a sandbox full of optional quests. Outside the main track, you can play at leisure and experience each of the characters. Each mafia has it's own set of stories but does not block you from the other character stories.
It's his coding and code management that is out of control. He definitely needs to spend more time cleaning up the many bugs before introducing so many more. Most of them are painfully obvious and there is no excuse for creating a release with them.
Finally, it is very obvious that BoN is doing a good job with the stories. If he wasn't, people would've abandoned this game long ago for the bug load and current save file editing requirements. Since he has such a strong following, it shows his stories and characters are worth the troubles.
Oh yeah, I almost forgot. The post to which you replied had nothing to do with whether or not the pregnancies were acceptable, believable, or even good story-telling. He was simply answering a question about who had gotten pregnant in the game so far, according to the sperm/egg image, a topic your tirade did not even remotely address.