This is a bit more of a long-term thing, but it would be interesting to have more variety in ship parts. Living ships for example, might have a different part/tech tree to regular ships, and would offer some visual variety, besides what paint and designs can do.
Functionally, they might be identical (for balance reasons), or have some different/unique weaponry that can't be obtained on regular ships, at the cost of not being able to use conventional ship weapons.