I absolutely love the Ship Designer. Don't get me wrong, my thousands of hours are mostly dedicated to managing empires or killing enemies or both, but I love the Designer.
I do not do "conventional" designs. I do off the wall things that convince me that they are not anything humans would build or that tickle some part of my funny bone, or most importantly, somehow leverage the animation portion of the Ship Designer. There are numbers buried in those animation settings! I am not an artist, but I am clever with numbers, so some of my designs are quite original and unique. Most importantly, even though they take tons of fiddling and rethinking about values and relationships, they are fun for me.
My highest praise goes to the texturing. I am almost always completely satisfied by the way two parts of a style match up no matter how you connect them. It looks like it was built that way on purpose, even if you don't know what the purpose is. That is an important illusion for standard designs and really helps my wilder ones. That it can work with so many physical placement variations amazes me every time. Even non-matching styles can be made to convincingly merge and do the "It's supposed to look this way." illusion. Nice. Thanks go to the Ship Designer designers.
Next goes for the number of variables in the design tools. Offsets are great. I don't always understand what is going on with Symmetry and my animations, but when they do work out, it is perfect for synchronizing things. The different animation motion choices are, of course, the key feature for me. I am still trying to figure what to do with animated scaling. What I have found so far is pretty wild, even for me. It is there in those animation settings I get the most satisfaction and the most frustration, all at once. We are all obsessive here, but we obsess over so many different things. 
Now for the frustrations:
I cannot believe there is still no cute stylized 3D compass rose marked Forward, Aft, Port, Starboard, Above, Below. That it is not there in a corner spinning around to match the way I have spun my ship model mystifies me. With each patch and release I look in the corner for it, but it is not there. If someone can explain why it is not there, I would love to hear that. I know it has been mentioned before on the forums, and if you devs claim to be listening to us, this is not evidence that you are doing so. I am still disappointed it was not part of the original plans. There is not much about the game I would say that about, but that is a horrible gaff in my opinion. A similar one is the scaling issue. I have a Medium hull that almost spills out of its hex tile on the map. I have no idea how to fix that and I do not appreciate that the designer did not give me some clue about it before I put all my work in.
I have lost many ship designs because I forgot to save the test file game I was using to design the ship. I still don't understand if I should save as template or save as ship or what the difference really is. I get confused about the custom parts function, and it doesn't seem to like saving animation definitions. The busy work of ship designing could use some streamlining or something. I generate tons of interim files during my designing and cleaning them out is not really an in game function. And I still haven't heard why the Ship Designer can't be accessed from the main menu.
When I get down to the details of the animation settings, I do not understand many of the decisions made there. One is granularity. I can adjust Rotation in integer steps from -180 to +180. That is a lot of freedom of choice. But it is not as much freedom of choice as implied by putting a decimal place in the display. As far as I can tell, there is no way to utilize that decimal place. I don't know why it is there. I would love for it to be meaningful, but I doubt a lot of other people would notice. Either make it do something or get rid of it as an empty promise. When I go to Lateral motion I get a range of choices from -10 to +10. Why is that? Is lateral motion somehow different to code? And again there are decimals there that should help my nitpicky obsession, but they don't do anything. I type them in as values and it looks like it takes it, but it is a temporary illusion and does nothing.
In each of the animation screens there is a function called Oscillate. It is a wonderful idea and very useful. Setting it up is a fiddly mouse movement pain. If I need two parts to move the same distance, I have to set the two arrows exactly the same on both. Neither arrow lets me set the value precisely with the scroll wheel. And in the Lateral movement settings, I suddenly have functioning decimal places! Yay! However, it has its own ideas about how I can use those decimals and will jump from 3.2 to 3.6 or some other interval. But I cannot enter numerical values and the scroll wheel does not slide the arrows, so I end up trying multiple times to move my mouse just one pixel and get this part to 3.2 just like I got the other part. That takes a lot of the fun out of the process.
I could use a button that resets the animation to start point and pauses. Otherwise, adding parts becomes a nightmare. The present pause button can leave parts in positions where the hardpoints are not where the part is visually at the moment. You get unidentifiable hardpoints floating in space.
I could really use a phase control function to synchronize or de-synchonize two matching rotations. I consider that a request for a very limited usage base but having one object pointing forward while the others are pointing starboard is a problem. You can often fix it with a quick static rotation in the Edit function, but in any compound set of rotations, a simple phase adjust, even of 90 degree steps, would be a big help.
And I want blinking and dimming animation for glowing parts, pretty please.
And I want to end on a high note. The Ship Designer can be very interesting if you let someone young coach you as you design. "It needs more glowy things! Make the top part spin real fast!" "I want one of those!" Fun.