John Barrowman has talked about being disappointed he wasn't asked back for the show's 50th anniversary. Could part of the reason be Torchwood; Miracle Day? The scale of it felt ridiculously large, which makes the Doctor seem somewhat villainous by not intervening to stop the unnatural phenommenon. The events of Miracle Day are never referenced on Doctor Who, although the dates of some episodes overlap.
So if Captain Jack were to return to Doctor Who, they'd have to make some attempt to reconcile the events of Miracle Day. RTD, BBC, & Starz have been noncommittal about whether Torchwood will return so Moffat doesn't have unlimited leeway in deciding the Torchwood status quo. He could say it ocurred during one of the alternate bottle timelines in series 5 or 6, but that might come off as disrespectful & hurt the future viablity of Torchwood if it's no longer canon to Doctor Who.
