I never really used the ship designer in GalCiv2.  This was due to it seeming really strange to use when I loaded it.  With this being said - I gave this a try and fell in love with it.  I can't compare the two because "something" in the last game turned me off from experimenting with it.

So - from a first time Shipyard user, here are my thoughts:

• I really like the rotation dials.
• I like that you can change the snap options for offset, scale, and rotation.  I didn't realize this at first, and was frustrated with how much the dial jumped when I dragged the slider.  I also didn't realize you could click the left and right arrows to fine tune these numbers.
• When inputting numbers on Offset and Scale, they don't commit if you click in space or hit tab.  I had to click on another number to commit.  I think committing by clicking anywhere on the screen would be better.  Also when clicking on one of these numbers, I think it would be better to have the whole number highlighted rather than inserting the cursor.  I think it'd be quicker to just type in a new number.
• Oscillation is fun!
• I love all the parts.  This will be a lot of fun to play around in and create some pretty cool ships!
• I noticed that when I would place a part, the X,Y, and Z axis were dependent on the part in question.  For instance, the Y axis might make the part go up and down, diagonal, sideways, etc.  I think it would be easier to use if these axis' were universal - as in to space in general - rather than the part being used.
•  I didn't really have any issues with hardpoints.  I found that the offset dials negated this.  
• This is probably a stupid suggestion, but when I made my ship, I was surprised how tiny it was.  lol  Maybe a button or something to show a overlay of a ship such as the scout or something would be useful to compare size.  
• I almost think having up and down spinner buttons next to the numbers on scale and offset would be better.  Or make the left and right arrows stick out a bit more.  

That's it really.  I have been having a lot of fun messing around in the shipyard!

Here is my pathetic ship: