Cogenitor was awesome and absolutely one of Treks 10 best story ideas. It was also quite original.. all the great story ideas I've thought of to post here weren't very original.
The Borg were a great idea too. At their best they were both terrifying and full of pathos because you knew that drone was once a person like you and might still be a person somewhere deep inside, under all the circuitry. And yet the drone's mission was to take away your own personhood in the most horrifying way.
As a true Borg enthusiast, I can tell you that what you just wrote is positively correct. And that is why, I think, that people are drawn to the Borg. We relate because the Borg drones were and are people like us, assimilated into a world of the Hive Mind and unified "individuality" in the hopes of achieving perfection. We fear them because, in their drive towards universal perfection, they are required to take our individuality away from us; but at the same time we empathise with them because they were once individuals like us, with emotions, hopes, dreams, and Life.
So I agree 100% that the Borg were a truly unique and creative idea and theme, and should definately be up there on the charts!
The Borg, I agree, are a terrifying concept. The absolute antithesis of individuality, of freedom of thought. It's very fitting that they were created in the 80s, a decade where we were still very afraid of technology and the effects it would have on our lives. Many films of that era use that theme (WarGames, Terminator, etc).