The first three stone ships aren't really particularly good and I think skill with those sections will just come with time.
The bioship is plane generic and the bone ship is... erm... odd.
I do see some merit in the vulture design in fact I'd actually go as far as to say its good. All it needs is some shading as at the moment its just a dull lump of metal.
Mass shows some interesting part usage and the engines are well constructed. I think really if you shoved all the parts together and didn't have the gaps then it'd be at least a decent ship.
I thin the main problem you are having is that your not setting yourself at the right level. You've lurked on this forum for a while, and I take it your an avid sci-fi fan. Because of this you are trying to build huge incredible super-ships that rival the star destroyer executor in detail and just ending up with alot of bad ships, because you simply just don't have the skill. Try to stop yourself from getting out of your depth design a simple ordinary fleet starting with the frigates and then slowly move up the ladder until you finally have the skills to build, and I quote, "the most epic thing possible, PERIOD." And that will happen eventually.
On a final note just think about this Anna and Arcalane were noobs like us once too so keep at it.