Add in the cardassians, you could easily make new ships for them, and keep the galor and other lock box ships as like retro ships, say there military has advanced past such antiquated vessels, and maybe even allow them to ally with other factions like the romulans.
Dominion, again add new ships and say they phased out there lockbox counterparts, they rule a massive area of space, and probably have access to other ships and races we havent even seen yet, add all that area in, and create a story about the dominion coldwar still going on.
Borg, I know Iknow, but it would be an easy faction to make, with an option later on to be liberated or stay with the collective, giving an insight into how the collective works.
The breen, seriously, theyve never been touched, like noone knws even what they look like, it would be a great faction to make.
Tholian, yep, they would be awesome, and you get to make even more tholian ships, and there fleets should have an annex world option, and you could get slaves and stuff to work in your dilithium mines by donating special slave duty officers that could mine you like 100 dilithium a day for three days, then they die, plus it would give insight into tholians and could make for some interesting story telling.
Voth, I wanna be a dinosaur, and fight in the sphere.
Undine, I wanna be a giant 3 legged monster, and learn there story, plus fluidic space would be a nice new place to visit and explore.
Mirror Universe Terrans, add in all the federation sectors for missions, and tell a fan favriot story of the wars in the mirror universe,and even play as a terran captain, and come through into the prime univrse, that would be so awesome.
Feringi/mercenary, A faction the has a huge variety of races and ships, classes include Mercenary/Engineer, Pirate/Tactical and Rogue/Science, and there pricipal fleet objective is to form a corporation, with several aims from contracts to all the different factions fleets, to raiding civilians, and being privateers, and they could have a very good story about establishing a criminal empire on Nimbus, thus doing something useful with that boring zone.
Next GROUND VEHICLES :)
Seriously add the argo, and some type of tank, get creative, go nuts with all the factions, add everything from jet packs to mechs, and even sell some for zen, buy make it for ground adventure zones only.
Next NEW ZONES AND PLACES
We want more adventure zones, both in space, and on the ground, we also need a gamma quadrent and a delta quadrant, plus mirror universe places, andfluidic space places.
Next GROUND COMBAT REWORK
Not as in how it works, but things like being able to call down way more security officers, because you cant tell me on my carrier with 4,000 crew, when i go assault that orion base i only take myself, and 4 officers, no, I should be able to call down more squads of just guys i cant customise, and give commands from a tactical overlay, just rework the map to act as that overlay and add in the mechanics, maybe a limit on guys based on your crew size, and have a much better strategy game.
Next LEVEL CAP INCREASE TO 60 WITH COMMANDABLE FLEET
Yep, increase lvl caps, add in some new abilitys for lvling, and be able to promote your officers to captain, and put them in command of ships in your ship yard, you can set there equipment etc, and there abiltys still from your new battle group commanders tab, but when and how they use them is up to the AI, and then have that same tactical over lay i just talked about, and be able give commands to your ships, trust me when I say this will boost ship sales, and bring more players in, not to mention all those lock boxes people will now have to open to get gear to outfit there new ships, but for the love of god dont raise equipment teir, or people who have spent a lifetime on this game and aquired all the best high lvl gear will quit, XII is high enough ok, but with the lvl increase you could realeas that shiney new jupiter class, nudge nudge wink wink.
Next DUTY OFFICER REWORK
Add in new stuff to that, more officers is great, but add in a staff tab, for what you put the officers over, and an assets tab, for vehicles and stuff, a freat way to explain this is by how it wuld work, so heres an example, You want to start a diplomatic mission, it requires 2 diplomats, which you have, a security officer, which you have, a security team, as your staff requirement, maybe well say the name of it is 121st MACO strike team, next it requires an asset to get there, you have the runnabout asset USS rio grande, all these things will affect the outcome of the mission, and yea.
Assets can be anything from starships to argo buggys, and you can only have 100, and 100 staff, staff are going to depend on the mission type, but can be maco teams, medical teams, marauders, engineering teams, to Gurilla fighters and refugees. Assets in the form of starships however can be equiped like duty officers to your ship, each taking up a set number of slots of which there are 5, and you cant equip two of the same, say you have a soverighn class, and two miranda classes, whatever there names are, equiped, when you call fleet support, those ships come to your aid, I know thats a genious idea right,
Finally when ever you send out a duty officer mission, if its on a small craft asset like a shuttle of fighter, you should see it fly out of your ship and see it travel to the edge of sector space and vanish, plus add in more random ships just cruising around in most sectors, gives them more life.
Next CARRIER UPGRADES
Increase the number of pets fieldable from hangers from 2 to 3, and the increase the number of ships for some squadrons like peregrines, toduge, and runnabouts, pretty much everthing thats a squadron, instead of a single ship like the bird of prey, by one, trust me♥♥♥♥♥soon as fighters are viable and do something youll see ship sales increase dramatically.
Finally CROSS FACTION PLAY
As soon as someone gets to a certain point in the story allow them to que up with friends who are playing a different faction for pve