One thing that strikes me as a necessity for this game is a deeper variety of missions, otherwise it will just degenerate into a slugfest. More variety, more interest in the game, and the ability to hold interest longer.
So, I've started to come up with a list of missions that should be available.
Patrol: The most common mission. This is not to be confused with the SFC2/3 Patrols. In this patrol you are given a start point, and an end point. While performing this mission, your goal is to note anything out of the ordinary, and investigate it if time allows. You will have to complete your assigned patrol in a specific time frame in order to achieve mission success. These are also meta missions, unless you are re-deploying, re-fitting or repairing, you'll likely be on this kind of mission.
System Survey: A Charted, but unexplored (recently) system is nearby (or along your patrol route), take time off your patrol and investigate every body in the system, planets, moons, asteroids.
Follow up Survey: A previous system survey noted something in a nearby system that merited further attention. Your orders are to go in and conduct a thorough investigation, complete with landing parties, if necessary.
Convoy Escort: Whether it be Orion activity or a hostile Empire, a Convoy needs an escort from point A to point B. The Convoy will travel that distance at Warp 2 (High Tactical Warp), and will automatically slow to sublight speed if a hostile gets close enough. You can leave the convoy if you feel bold, but the convoy must arrive at point B otherwise you will not only gain no reward from the mission, you may be punished for abandoning your post.
Planetary Assistance: Whether from an Orion raid, an Empire assault, or even a natural disaster. Your mission is to arrive and provide assistance.
Pirate Hunting: Orion activity in the sector has reached a point where your empire has decided that it needs to be dealt with. Hunting down an Orion raider or base will go a long way to restoring order to this sector.
Establish Mining Facility: A follow up survey has noted that this system contains materials worth exploiting. Escort a pair of construction freighters and protect them while they are constructing the new facility.
Listening Post Upgrade/Repair: A listening post has been damaged or it is due for an upgrade to its sensors. Pick up the parts from a nearby Base, pull up along side the Listening post and send over engineering teams to conduct the upgrade/repairs.
Establish Colony: Whether its a beautiful M class planet, or a wasteland that just happens to occupy a strategic location, your Empire has decided to found a colony here. Escort the homesteaders to the new planet and defend them from predators while they establish their planetary defenses.
Base Construction: Your Empire has decided that a Base in this area would assist in the completion of other missions, and would provide added security for this sector. This is a long term project, you are only required to be present for a portion of the construction, after your part is done another ship will rotate in to relieve you. You will either be asked to escort the construction freighters and oversee the first stage of construction, oversee a stage of construction, or oversee the final stage of construction and test the operational status of the base.
Base Defense: A Base's normal defender has been called away from some reason, or the Base Commander has requested temporary reinforcements. Either way, you are being temporarily stationed here to provide additional defense for this base for the duration of the "crisis". The crisis can range from a conference being held on the station, to an Orion attack, to an outright assault from another empire. It can also end when the normal defense ship returns from whatever mission it was on.
More to follow, but kids are pulling me away from the computer for the moment.