If I had my way, I'd strike Jack from the record after Empty Child/Doctor Dances. I'd even settle for his disappearance after the season one finale. And the reason for this extreme distaste?
Jack flirts with everything. Like, everything. I don't watch Doctor Who for the romance in the first place, and every time Jack reappears, I feel like it slips into a reality dating show for a little bit--even if the Doctor immediately tells him to knock it off. Jack has to be the only man who can make "Hello" sound dirty.
To be fair, he doesn't seem the sort to force himself on anybody--but that hardly makes it better. Of all the new series companions, he's the only one I would REFUSE to travel in the TARDIS with. I mean, some I'd like better than others. But if the Doctor showed up with Captain Jack in toe and invited me in, I'd say. "Him or me."
I haven't watched Torchwood (although I'm more tempted since the demise of SJA) and the general sexing up of the Whoniverse disgusts me.
Jack should really be more careful with this new version of the Doctor. Sex-free crackfic