I think putting the face onto the source is what made it lose the value, unfortunately.
My comparison is what they did with the Borg and the Queen. Wolf 359 is a terrifying, tragic ordeal, made all the more serious by the fact that it was done by one cube that could not be negotiated or reasoned with. As soon as the Borg had a way to negotiate and reason, they became less scary because they had understandable motives and goals that could be bargained with, as excellently demonstrated by Janeway.
Ultimately, I agree with you that it's kind of more of a TOS-y sort of plot device. I do feel like back then they really followed the science being indistinguishable from magic logic, and we've progressed over time to wanting more hard and serious technobabble. I think that's kind of a disconnect for me, personally, is that they had to dip into a serious explanation for something that effectively functions like magic.