Try Suicide Junkie's Pirates & Nomads mod - the missions are the same as the regular game, but the ship components are all changed around: armor is much tougher but nearly impossible to fix without docking, weapons are more varied (gatling meson bLasters anyone?), crew quarters provide minor repairs and actually increase the crew capacity of your ship...
Get it at SJ's site:
http://imagemodserver.mine.nu/other/MM/SF/mods/
You'll need WinRAR (shareware) to extract the archive file (I think you extract it into your Campaigns folder under the main game folder):
http://www.rarlabs.com/