Right. I was expecting the Preservers, mysterious and powerful, but biological aliens nevertheless.
I've been thinking some more about those two examples in my first post, and it's not the case that they break our reality, but that they break the rules of Star Trek's reality. Deliberately I think. First was the asteroid that couldn't be teleported by the Magic Save The Day device – you know, the transporter – a development presented as so shocking that it was used as the act break. Of course it didn't turn out to be magic, just a new scientific development that had to be understood, but it was something the Star Trek reality hadn't seen before. It took work to understand.
Then there was New Eden, where the inhabitants became more, not less, religious as a result of encountering advanced extraterrestrial intelligence. Trek has generally held to the idea that as humans expand into the Galaxy, we'll become more secular, and has implied that secularism is required for peace (see: Who Watches the Watchers, where the Minitakans are willing to commit human sacrifice as soon as they get religion). But in New Eden, the colonists are peaceful because they've blended their faiths.
Both of those challenge certain conventions that Trek relies on, and I don't think it was unintentional. IMO, it was a statement about where the season was headed, and I think it's probably poorer for choosing Space CIA vs. Skynet instead.
