I think the fundamental problem with Torchwood is that it's really two separate stories that they forced together as one. On the one hand, you have the "Secret Society" story with Torchwood collecting alien artifacts and 'secretly' defending the British Empire against aliens. On the other hand you have the "Captain Jack Harkness" story where Jack has adventures. I think it was a mistake combining them. Torchwood should have been more X-Files - dark, gritty, conspiracy, secret, etc. The Jack Harkness show should have been, well, Jack doing what Jack does best - getting into, and out of, scrapes. It would have been fun if his Vortex Manipulator still worked and each show he ended up in a different time/place. The Jack show would have certainly been a lighter tone, more jovial.
The problems with the first two series can be summed up in a line from the pilot: "Who orders pizza under the name 'Torchwood'?"
Or, conversely, maybe you do put them together but Torchwood is the antagonist and Jack is the protagonist that travels through time trying to "fix" what Torchwood breaks (Doctor Who meets Quantum Leap).
Personally, I wasn't a fan of the last two Torchwood series. Children of Earth was very well done, but it was too depressing. So, what do they do with Miracle Day? Lets make it MORE depressing!!! Torchwood was at it's best when it was fun with dramatic elements.