While you're getting your bearings, send our Seekers or other recon vessels to give you a picture of the surrounding area outside your immediate sensor range.
Manage your resources carefully to make sure you can build the ships you need when you need them. A good rule of thumb is to ask yourself, "Do I need this module/upgrade/ship to complete this mission?" before building it.
Upgrade only the modules you need to complete your mission. If you try to upgrade everything, you won't have enough resources to defend yourself.
Focus on defense first, then offense. Don't fall into the trap of creating a strike wing before your ships are adequately protected. You will have time to build more ships if you live longer. Build a defensive screen of fighters around your Command ship before worrying about a strike force.
Upgrade ships as soon as possible. Examine the mission profile carefully and upgrade any ships that have abilities you'll need.
Protect your assets. Just because you've built a powerful vessel, don't get cocky and put it in the vanguard of your strike force. The more costly a ship is to produce, the better you should protect it with other ships.
Deploy strike craft in large groups. A little bit definitely does NOT go a long way in this game. If you're going to attack, then amass the biggest strike force you can afford to get the job done right. Keep them in dock until you have amassed enough to defend if that's why you're building them.
Vary your formation to fit the target. As a general rule, Claw formation is best if you're up against fast-moving craft. Use Sphere formation against slower moving craft that don't have weapons that fire in multiple directions at once. Wall or X formation is useful if you want to focus fire on one area of a ship, such as the rear or flank.
Disable Command Ship modules first. When fighting against a Command Ship, target their modules first to deprive them of Support Units.
Destroying the enemy's ability to gather resources is key. Take out enemy Workers and Resource Processors quickly, and stake out resources with your own vessels to deprive the enemy of the source.
