You'll have to forgive me. I just got done with a really bad movie when I wrote this and it really ticked me off.
It's important to know the difference between doing something and doing something wrong. This is where many of these stories fall short. Let me give you an example.
In X story, Sam decided he wants to study black holes. So Sam builds a device to generate black holes for him to study. He creates a black hole, the story asserts via narration that there are some things man is not meant to know; it ignores the insane black hole device and jumps straight to the assertion that man was never meant to know about black holes.
This is only an example.
This is the standard formula for a science gone wrong story. I'd like for someone to write a story where A) The overall goal is not condemned but the reckless actions taken to get their are highlighted as a morality tale. Or B) The Creation itself is inherently flawed, not the means it took to get there.
Creating an intelligent being--as in, one capable of thinking for itself--only to force it to obey your every whim? I can only see good things coming from this. Slave rebellions never happen in real life.
Yeah, I wasn't vary clear about that Lovecraftian thing. But, basically, you got it: a story that teaches people to embrace and be fascinated by the unknown, where the villain isn't the strange and unexplained but a man or group whose fear of the unexplained might doom an innocent. I shouldn't have to tell y'all not to use a religious organization to do this. If anything, make the bad guys pseudoscientific "Philosophers", much like Lovecraft himself.
You know, E.T. kind-of follows this formula a bit... Huh. But I'd still like to see more of this. Better to do it without the cute alien anyways, as the message could kind of get lost. Have it be an unexplained phenomenon or some incredibly strange and alien creature. Something utterly strange: An alien that ultimately proves itself to be beautiful; not necessarily beneficial, though just beautiful in its own way. Beneficial does work, but it hammers the point too far into a preachy territory. Benign and beautiful has a more subtle a sensible feel to it, but that could just be my opinion.