The better you handle each situation (or how many violent ships you dust), the more points you're awarded at the end of each mission. You can put these points into the ship's functions, so that phasers and shields regenerate faster or your turning ability gains some speed. Most of these techniques are upgradeable, so you can pump all your points into weapons or go for maneuverability.
If there's one thing (other than the flat-as-hell combat... we’re never going to let that slide) that we'd like to see improve in Assault it's the overall presentation. Sure, we get some nice memorable quotes from the series on the loading screens, and the sound effects ring true to the shows, but the bland menus and lifeless mission briefings are going to put people to sleep. It's enough to keep the Trek diehards happy, but are there really that many left out there?