There is a fog of war in the game that limits your ability to see other ships. In addition to the waypoint system, a new slipgate system is included in the game that allows ships to hyperspace jump between fixed points in space. These points are pre-defined on the maps and you must find them in order to use them. Once found, they will be displayed on the sensor manager screen. A new resource crystal is available for harvesting when you have a certain level of technology to do it.
Crystals yield more resources than the normal source.
The skirmish AI against computer opponents is improved but still has some holes that were found in the original. The computer does not do a good job of managing the somewhat complex technology tree and this can lead to strange results. Special ship functions just do not seem to be part of the AI's decision choices. You can use the resource injection option that gets rid of the harvesting function and each side is given a set amount of resources that is provided during the course of the game or as a lump sum. This makes the skirmish games more challenging as the AI has one less thing to manage in the game.