I think I know what he's talking about with upgrading a ship design, but still having to manually assign its construction. When you go to update a design, and you "clear" it in the ship designer, the game behaves as though you're creating a totally new design, and thus doesn't switch your spaceports to the new design after you obselete the old one.
I figured that out when I had to whack the "Clear" button on the core designs when I tried updating them in 1.2 Beta 2, because I couldn't remove any of the components (I'll have to go post about that in the appropriate bug-report thread).
As for not using the same name, it's really not that bad... There are many ways you can denote different versions of a ship without using numbers.
Instead of Constructor, then Constructor MK 2, and so on, why not something based off generic terms for contruction, like: Constructor, Crafter, Builder, Erector, Infrastructor, and Creator?
Alternatively, you could use professions, like: Constructor, Carpenter, Sculptor, Mason, Artisan, and Engineer.
I once made a frigate that resembled the shape of a claw, so I built off that to easily get a name for it and it's upgraded counterparts: Laser Claw, Plasma Claw, Phasor Claw, and so on. Obviously, they were armed with their namesakes.
I like using themes for some races, too--the Korx are (at least in my mind) radically capitalist, so I give their ship classes names like Establisher, Franchiser, and Monopolizer. The Drath are reptillian, so I name their ship classes after various real and fictitious reptiles.
Of course, sometimes you just get really stumped as to a good name for your new design; when that happens, I'd suggest perusing the pages of a thesaurus, or a multilingual dictionary.
