It seems that they added the 'feature' where when you go to upgrade a starship class in the shipyard, it automatically strips off all of the stuff you had on there before, which is annoying. VERY annoying. What happens if all you wanted to do was switch out weapons? Now you have to add all that stuff all over again. This should be an optional 'feature' you can switch off in the game menu. All they needed to do was put an extra button at the end of the little parts scroll to 'jump to end' so you don't have to manually scroll through it.
Also, a feature to filter out custom ships you've made based on size category would be a lot of help. I have made a lot of different ship classes, each having a different specialty, and even after obsolescing all the old stuff, 20-some odd ship classes is still a lot.