Inspired by this post:
http://forums.startrekonline.com/showthread.php?p=3116662#post3116662
I would also post my personal wishes I collected since closed beta. Some points are not my own ideas.
- Visibility of injuries on the scanner (shows where it is located), or for the future real visible on my ship/body
- Possibility to heal or repair injuries on sickbay or shipyard (for free).
- Equipment injuries, Weapons will get also damage, could burn out or something (could be repaired with components or in the engine room)
- BO's will get my uniform as default uniform or a button "take captains uniform".
- Spacesuit Missions, interior and exterior, low gravity.
- Visible medals on the gala uniform for our accolades. Three definable slots.
- Disassembling of items into their materials/components. You could use those materials to build new items.
- Upgradeable items, using components or data samples. (Weapon + Compontent + Energy Cell)
- Craftable Kits, assembling different buffs of your choice to create my perfect kit (must be really expensive).
- Special fractions: Trader (Ferengi/Karemma), Freelancer (Hirogen, Multirace)
- Database in the sickbay or containers in the cargo bay to store data samples/traces.
- Commodities/Food/Components should be storable in cargo bay-containers.
- Randomize the stats of the looted and crafted items. Define a range from +1% to 10% for each value.
- Melee weapons like: D'ktahg, Kut'luch, Mek'leth, Lirpa,...
- BO-Templates for several species like Hirogen, Vorta, Jemhadar, Cardassians...
- Inship Missions (eg. Beam up some wounded to my sickbay and then take care of them)
- Adding an Arboretum, Shuttle bay, tactical bridge,... to our interiors.
- Minigames
- Minigames...
- hmmm... I mentioned minigames already?

- Interaction with ship systems, beaming from beaming room, using the replicator in 10forward, reading mission logs and contact Starfleet from captains room, switching clothes in captains quarter
- Additional professions (Crafter (bonus on memory alpha), Trader (bonus in stores), Researcher (Improving items), Trainer (more damage to meele attacks)...) could also be handled by unique skills, its only allowed to choose one direction, or you handle it like the diplomatic career.
- Scaling the Fleet symbols on our own, its too small
- Jamaharon state on Risa
- Earth needs Rotation and day-night alternation (and hopefully sometimes a social area)
- Weather, Environment, Radiation will affect your weapons and shields (EVA needed)
- More Pets, could take care of them, feed, play, and train them (they could give us some buffs) or could live in our quarter
- Musical instruments (playable with a minigame)
- Special Holoprogramm to test Weapons and Items... "Fire 5 Torpedos to the asteroid" (I think that could be handled by the foundry)
- Vehicles
- Attacking Targ our Bloodhound-Targ (which could find enemies on a map)... Ive seen that we could get some targbreeding-thing, that would be realy cool.
- Harvesting
- Housing, arrange your furniture, design my room... (also foundry...)
- Autopilot (switches instances on his own) or a better galaxy map where you could search for your target system and it will visible on the map
- And one of the biggest points, already seen in the forum for several times, traveling through the galaxymap from bridge... set course, and have a look to the stars, contact starfleet and analyze the systems and other ships.
There was alot of more, but some are already implemented, anounced or definitively noticed. Thanks

And please have a look to my signature-topics...
Comments
How do you know what I am wishing for STO?
Are you a betazoid?
Don't forget an option to select a "standard" uniform for all the NPCs wandering on your ship.
I think that issue is already adressed... one of the devs talked about that.
harvest from astrioids or caves.. especially with those new "little fractions" dstahl talked about...
A Harvestingfraction, they got special ships to get some special anomalies or materials.
Check my crafting thread for more info about that.
This I would like to see, but modified. At the tailor there should be two additional slots. Crew Male and Crew Female. By setting up these two uniforms, you set up the uniforms of every crew member on your ship. That way you can go back and change it if need be and if you change one, you change them all.
something like that is already announced, the first officer system... you could change your 1off into a playable char and as I understand that right, there will be a possibilty to own your own little fleet... like your offs running with you on the groundmissions, they will join you during spacefights