Gemini tends to have backwater ships because it's not really a frontline sector. Gemini's off the path of the war, really, even though there's a bit of a Kilrathi presence.
Basically, between WC2 and 3 there were End Run and then Fleet Action. At the conclusion of End Run, Confed had evened up the odds a bit and in the process had hit upon a successful strategy (hitting supply lines and deep raids with escort carriers.) Far behind Kilrathi lines, there was a secret construction facility. It was taking a large number of transports and resources. Because of this, the Kilrathi were unable to properly supply their combat forces. To buy time to complete the super carriers they had secretly under construction, they pushed for a cease fire. Eventually this resulted in the signing of a document which made each side promise to stand down large parts of their armed forces. Pretty much all of the Confed carriers were put into mothballs, and their cores shut down. A while into this, Tolwyn, Paladin, Hunter, Bear et al. managed to find proof of the Kilrathi plan through rather daring methods. So, Tolwyn rushed back to Earth, only to have a high ranking Kilrathi blow up a large portion of Confed's high ranking officers before he could warn them. Tolwyn was put in command of the fleet and rushed to get it ready. Basically, it resulted in the Kilrathi getting all the way through to Earth before finally being pushed back through a series of rather dramatic events. Confed defenses had been pretty much raped and only a couple of fleet carriers remained. By WC3, old ships that had previously patroled backwater systems have once again been forced to become front line vessels,