Is there anyway to remove abandoned ships from the game? As much as I love the flavour of exploring and finding scattered relics and ships I feel they throw off the balance of the early game way too much.
Other than using the editor and going around manually deleting (which is very tedious) them I don't think so. For a strategy game there's far too much randomness in DW, it's part of it's charm at times, but I know how you feel.
Turning off the storylines will get rid of most, though not all, abandoned ships, including the big treasure troves (debris fields, strategic reserves, and similar).
I like the crazy imbalanced randomness of the universe in DW. If the starts were balanced, the AI would never be competitive with the player without getting massive bonuses. With wild imbalances, some of the AIs invariably get a legitimate head start on me without them having to cheat massively.
My favourite example is still the game where a minor race grew to full empire status, then got lucky and immediately discovered Way of Darkness and grew to become the main evil juggernaut of the galaxy.