I've seen the same thing - newer versions of Makerbot Desktop seem considerably slower than the older Makerware. If it's an option (meaning if you don't have a 5th gen machine), you might get faster slices by using the most recent version of Makerware - there's a link to it in one of the other threads on this board.

If moving to an older version isn't an option, you could try Matter Control's beta x3g support. Alternatively, there's a way to use Slic3r with Makerbot machines (full disclosure - I have only tried this with a Replicator 2X). The method is documented here - http://www.3duniverse.org/2014/01/05...forge-creator/.

Good luck!