i always subscribed to the yorktown theory. yes its a little grim that the crew might have perished and they are getting a ghost ship, but it can explain a great multitude of things in the next few movies:
the pristine condition of the bridge at the end of TVH = starfleet gave it a good scrubbing after the events of the probe crisis and yorktown crews demise.
the problems in TFF = issues with equipment failing because of the probe and/or yorktown's crew doing whatever they can to survive
the retirement of the enterprise at the end of TUC = its an old and now severely damaged ship
granted nothing backs up this theory, but it plausible.