The new logos sport a very smooth vector look which loses all of the character that the previous logos possessed with the bold, jagged shading. The skull looks generic, and the outer black outline in the flag logo seems a bit too thin. The flag is also too smooth on the top, bottom and right hand sides. That was definitely handled better in the previous flag.
The ship logo is now a lot more detailed which does not help the design at all. There is something to be said for simplicity, and the bold minimalist style of the previous ship logo was genius. The new logo does not even come close to being as good.
The old logos had some flaws of their own as well. When you take a closer look at the skull, there was something odd happening with the way the teeth were illustrated one way on the top row, and a different way for the bottom set of teeth. The shape of the skull around the cheekbones could have been a bit more refined as well. The only thing I thought the previous secondary logo lacked was a hint of waves towards the front of the ship.
Overall, the redesign just doesn't seem to cut it. Despite the few issues they had, the old logos were far better than the new ones, which now look like cheap vector clipart that you can buy off of any stock image website for a few bucks.