Here are some ideas that I think would make this an even better game. Oh and it's 5:00am so please ignore any moments of babbling.
It would be nice if the game acted more like the shows. Instead of us clicking through a bunch of names in a box to get missions we could simply have patrol areas where we stumble upon mini-missions as well as receive contact from starfleet and other "mission givers". Science ships get scientific missions, exploration ships get more exploration missions, cruisers get both exploration and tactical, while escorts get pure tactical battle missions. We are offered those mission on a take it or leave it basis right at that moment. This would be exactly like the show or movies where, for example, the Enterprise is patrolling a sector of space and a priority message comes in from an Admiral directing us to another location right that minute, they receive a distress signal or some type of sensor contact which could be a simple aid mission or could be a trap laid by enemy players for a raid pvp. There can be consequences for taking or leaving a mission. If you take an unethical mission it could affect your characters career development or refusal could make an enemy of the mission giver, if you refuse an important legit mission that too could affect you negatively where positive could be seen as a favor to the mission giver.
Allow more advanced and committed players to travel to the Delta Quadrant where there is much less Starfleet support, greater risk associated with gameplay but also greater rewards. In this sector there is more of a sandbox type of game play where there are no federation starbases but you do have the ability to buy, trade and sell items at alien bases, planets and transports for latinum. You could purchase weapons from liberatred borg, kazaon and other Delta Quadrant races. Perhaps this could replace the current Captains Table which does not really serve much purpose. Either the best players by skill level or Lifetime and long term subscribers are granted access to a rift which transports them to that sector. Getting back could be much more difficult. If you loose your ship in Delta Quadrant you loose that ship forever. The only way to get back to Alpha would be to buy an alien ship from a Delta merchant and then buy yourself a new starship once you make it back to Sol. In addition the manner in which you lost your ship could open you to further Starfleet reprimand.
A more effective choose your path feature would be nice. As in some other games, the way that you play could dictate your relationship with Starfleet, worlds, players, BO's and etc. If you are an aggressive player Starfleet will not call you to help mediate a dispute but instead will call you to help stop an invasion. If you break Starfleet protocol you can be reprimanded by the Admiralty possibly loosing rank. If you excel as a Starfleet officer you can be given special missions, rewards and etc. You could also become an enemy spy, a corrupt officer or some other unsavory type of career path. If you are bad enough you could be expelled from Starfleet and become a member of a Pirate syndicate, a reformed Maquis, mercenary groups, defect to the Klingons or some other entity. If you are good enough, but still morally ambiguous you could be recruited by Sector 31 for behind enemy lines activities such as raids on enemy fleet held outposts and other special PVP content. All of this could be done within the canon Star Trek universe.
This would encourage more fleet/clan involvement in the game. Also those who are not in a fleet/clan could act as mercenaries offering their services to a fleet in need for credits, latinum, equipment, weapons and etc.
If you choose to be a diplomat, you are not sent on missions to attack enemies, if you are a warrior you are not sent on diplomatic missions. As it stands now anyone can do any missions which negates any motivation to actually follow an in game career path.
This could really up the PVP content. Imagine a player flying around doing an exploration mission and an all points bulletin goes out requesting immediate help at SOL to turn back a Klingon invasion. An invasion which is made up of Klingon players who were recruited by a faction within the empire, could be a klingon player fleet or an AI. Spontaneous no queue PVP's in which your participation is rewarded or punished under Starfleet regulations. If you refuse to follow orders you risk courts martial, demotion or some other punishment. The individual with the highest rank is made the Flagship, or the entire group is split into multiple teams with the ranking member of each group being team leader.
Enabling the fleet holding the territory to rename it, place a large fleet logo, customize the territory and benefit from holding that territory would add to the community aspect of the game in a major way. Use the same type of raid PVP and wargame PVP content to enable fleets to capture and hold Starbases, outposts, mines and planetary bases strategically located throughout the game. A fleet that holds a starbase or outpost gains a commission from any exchange, merchant, gambling or shipyard activities at that base. A fleet that holds a mine or planet collects revenues from the gathering of resources and other business at that mine or planet. Any territory held by a fleet gives that fleet a base for which they can gather, socialize, play mini-games, hold war games, and etc. Bases, planets and etc. must be equipped with defenses similarly to the outfitting of a starship, i.e. orbital turrets, sensors and etc. at the expense of the fleet holding that territory. The reason for this is that other fleets will want to seize that territory, this could be a rival federation fleet via war games or Klingons via a raid pvp. A transwarp conduit, wormhole or some other method could be provided to the fleet holding the base so that they may get back to their territory in the event of they are warned of an impending attack.