The biggest and most obvious change is that the user interface has received a complete visual overhaul -- gone are the boring gray boxes, replaced with a spacey blue-and-green theme complete with sound effects and animations.
First, the player can no longer (by default, although this can be reverted in the settings) simply click on or drag a box around specific parts to select them -- the player must now hold the Ctrl key while clicking. This is because my playtesting showed that many new players would accidentally click on parts of their ship and then be unable to give their ship orders, which was confusing and frustrating for them. By requiring the Ctrl key be held, it's now almost impossible to accidentally select parts without meaning to.
Second, because you can't upgrade your ship until you repair it, the game now only shows either the repair button or the build button, never both at the same time. (When your ship needs repairs, the repair button is shown in the place of the build button.) In some playtests, players got confused about why they couldn't press the build button, and so this change should hopefully make that more obvious.
Lastly, turning on "blueprints mode" is no longer a strange toggle that appears next to the build button after pressing it -- it is now a simple checkbox item in the '...' menu, and the game now remembers your preference.