I gotta say that I'm still not a big fan of ship design in GalCiv2. And this is after designing tons of ships in other games...personally, I still think the "design by plopping bits onto the frame" idea is not a great one. It's not terrible or even bad, it's just not great. I can live with it though, especially with the option of just double clicking on the part to have it automatically added. The "extras" thing still doesn't do much for me, but that just might be a personal preference. I don't really feel like I have time to fiddle with all those bits, and it doesn't add much to the game. Aside from that, the number of red dots on the ship models is almost too much to even keep track of if you do try to design it from scratch.
I would prefer a ship design screen that had more obvious "performance" and size information instead of just the way the ship looks. Hell, I'd almost go so far as to say that the "tinker" screen be entirely separate, accessed by a button on the main shipyard. In other words, the normal design system doesn't require you to stick stuff on the red dots, but just automatically adds it. Then you can have a button that lets you go more in depth and add extras and move around stuff. Also, the slider for changing size doesn't always let you change something enough. That is something I just recently noticed.
Overall, the ship design wouldn't keep me from playing the game, but to me, it feels like more of a bother than a feature. Sorry for being a downer on the ship design!