This is by no means a complete list, but it's a start. Excuse the rant, but it had to be done...
- Core placement. The stupid thing has to be in the center of the ship or the ship rotates weirdly and looks terrible. It has to be accessible. It is the ONLY #$%^&* place you can fly the ship from. All of these things combine to make it an awkward piece of alpha game crap.
- Turret blindspot. Certain ship shapes do not lend themselves well to turrets. There might be one or two places one MIGHT look good. The problem is that while turrets rotate 360 degrees about their y axis, they cannot rotate 90 degrees about the x axis, leaving a huge blind spot directly above each turret. This means one turret on each side of a symmetrical ship will not give full coverage of the vessel, so you either leave the blind spot or find another spot to put a turret (looks flippin' UGLY on my current build).
- Turning system. No, it's not half-baked. It's FULLY baked. Anything but a doom cube is sub-optimal for maneuverability. Tear this one up all you want. There is no counterargument to this: You can fit more blocks in a minimized boxdim if said blocks are arranged in a cuboid.