OK, I've built a few dozen ships ranging from 'Awful' to 'Amazing' and generally, I hazard a guess when a ships is going to fall into the latter, or the former categories about 25% into the build, the trick is to know when to continue with a build to a polished model, whether to continue as a prototype, and not give it the same level of polish, or when to ditch your original vision, and try something radical with what you have so far. If you don't already, you should have a good idea in your head of how you want the completed model to roughly look, you can have this picture before placing the first brick, or come up with it while messing around with random constructions. Taking a picture of a spaceship you really like, and having that as a starting point from which to go to helps, while the goal isn't to copy that ship, it just really helps to start trying to do so, then branch off when your own creativity strikes. The best example of this in my ships comes from the second 'serious' micro-space ship I did, a little number by the name of the Vendetta.
This here is the Armageddon, and it's main features are a curved front, a long cylindrical like body, leading towards engines placed at the very rear.
This is the Vendetta, and you can see clearly where the vessel started life as, when these two are side by side, but at the same time, they are noticeably different ships, with different shapes used in them, and they have very different silhouettes. I started with 'The Armageddon looks dope' in my head, looked at why I liked it, and then went from there.
I'm not saying this is the only way to do LDDMS, or the best, but I don't think anyone will disagree with the fact it paid off for me.