An epic game idea.
Ironclad has shown its ability to walk a fine line design wise. I would say that they could actually tread the line between first person space game and grand space sim game.
Your ships would have to have the major defensive disadvantages of the sims game.
Capital ships could be multi person ships. Your carriers would be defenseless except for your fighters/bombers. A more complex system associated with antimatter than just "it recharges for free".
Ship diversification. Example: multiple types of lrms that perform the same primary function but then a unique secondary/tertiary function.
Good ship customization that provides real results and rewards for players.
Create interesting tasks for players on a single ship.
i.e. one person is a pilot, another the gunner. Give enough depth that both are fun 
Great for something like going Co Op with a friend
Much greater detail and expansion of the trade system, All items should be player made. Setting up a business. Decent automation of trade ships.
Ship capture options, with Space marine fights in a fist person shooter in the middle of a space fight. Compartments venting in space throwing you out to your doom (if without a spacesuit ) By the way, the anti boarding measures should favor the defenders substantially to deter boarding as a primary means of attack. It should be expensive and used against high value targets (capitals, starbases/stations, planets). Marine progression through these structures would reduce ship fighting efficiency until total control is achieved once the bridge has been taken. If the bridge is taken first, while the rest of the ship isn't under control the defenders still can prevent the marines from controlling the ship by cutting controls to the bridge and going "manual". Also secondary command stations could be a possible ship/station upgrade.
Have fun making that work Cloud computing better get here quick.
amphibious space to ground warfare. Just...why not. Ambitious, but its a dream that needs to see light in the industry. Put other developers to shame!!!!!
Expensive ships, Even more lucrative rewards. Trade lane control being critical to progression.
All ships should be controllable by a single person. one person could control a capital, but to fighting effectively with it should require a group of 5 people minimum, performing 5 jobs. More for repelling boarders (marines!).
Maintain the overall balance of the sins series for the higher strategy level play.
Good fleet controls to make the larger battles seem more "sins like"
Commanders have extensive fleet permissions.
An example of this would be:
A player joins the fleet to participate in an assault. First person in the group is the commander (can be shifted to another).
The commander jumps the fleet, basic navigation is under control of the commander until he is either determined to be inactive (5 min no complex activity) or battle commences.
Actual designed for game logistics software.
Commander/subcommander kill priorities to be sent to a screen in the players ship. lets say its a fighter. His squad is ordered to strike at LRMS. The player could ignore the target kill commands of the leader, to the benefit or detriment of the fleet .
Fleets need extensive organization. Good luck commanders!
Territory based empire balancing.
A single player should be able to accrue a sizeable fleet. The downside is that this fleet wouldn't have any pilots, so if it faced a fully human crewed fleet of equal size it would most likely get decimated due to the efficiency of player minds over AI brains. Likewise, a large fleet under the control of a single player should be able to wipe out a small fleet of players. This would be a delicate balance.
IP recognition/autopunishment software for some accountability. Only one account per person.
Welding in game. example, fly around in "space welding armor" and weld together the hulks that you have destroyed to create pretty pieces of scrap. then strap an engine to it and see your pile of junk fly through the heavens. Call it an ego boosting "prize ship" that has bits of many things you've destroyed in the past. Perhaps this could be the way players make cities in space. This would give people something else to do in an mmo setting then they have ever done before.
Useful, good parts scavanged from ships. So many games have horrible scavanging options....it should be worth it to have scavangers tearing hulks apart in the middle of the battle. scavanging should be one of the most dangerous professions .
