I'm a fan of both systems. When I first saw the ads for Traveller:2300, I thought it was a new setting for the Interstellar War era. However, the underlying assumptions for both are different enough that merging them is problematic. Everything from the aliens to FTL drive tech and vehicle tech is different. Even the tineline itself is off, as the Terran Federation of CT contacted the Vilani in, what, the 2100's?
CT and 2300 are very different universes, lending themselves to different styles of play.
I suppose you could merge them, with 2300 Earth being TL 12, no gravitics or jump drive. But I just don't see the point.