I rather like the new way of it, because it also allows me to change bits of jewelry to reflect a partial design change - after all, sequential upgrades of real life units look similar, but not EXACTLY like, the original unit. Josh_88's suggestion of waiting until improved weapons or defenses come along to add those as well. If you upgrade every time you get a new weapon, engine or defense, you soon become inundated with ship designs that may not be visible, but may become so the next game you play.
A compromise option might be useful however - giving the player the option to strip off parts or not would certainly be useful...
