I think one of the major reasons it comes across as really ship-based (which is one of the reasons I don't support it, I loved Ianto, but was meh about the ship), is because the ship's a lovely handy thing for them to hang their accusations of homophobia onto. The killing of the ship, the ending of the m/m relationship and the whole GLBT angle is the one thing they can really get on a moral high horse about, and therefore the ship is referenced at every opportunity.