Instead of just picking up where Children of Earth left off, first do an expanded season three. I think one of my problems with CoE was that it seemed so rushed. Rupesh trying to get into Torchwood, and Ianto's family, and Jack's family, and Jack and Ianto's relationship problems, and Gwen's pregnancy. I think that if there had been thirteen episodes to explore all these issues, I might have been more satisfied. So we might think about doing that ourselves.
Maybe start with the Hitchhiker that Jack and Ianto went to the hospital to retrieve. Expand on that story line a bit. Have a real Torchwood investigation that leads them to Mr. Williams.
And then continue with Rupesh actually being hired and brought in to Torchwood. Have him feeding information to his people. Think of all the drama when Jack finds out that he hired another traitor. This could bring up issues in Jack and Ianto's relationship that they thought were well behind them.
Draw the whole thing out to thirteen "episodes", with the 456 at the end of it. And Ianto still dying, but maybe in a more heroic manner.
And then Season Four, with Jack being all angsty and depressed. Then figure a way to bring Ianto back, because after all, it is Science Fiction.