Longer Time to regenerate hull damage - it seems to be as fast as shields
Medium Term Goals
Player Crafting/Economy (a la Star Wars Galaxies before they screwed everything up)
On named missions that are not repeatable, perhaps create a cinematic intro like the TV series. Make it an option to be able to bypass if wanted
Long Term Goals
If ship interiors are active, allow "Clans" to have the ship as it's base. In other words, all the positions (first Officer, Engineering, etc) to be players in a clan working together on one ship or possibly a fleet if the clans are bigger
Interactions with recognizable characters (in long term goals section as I would like to see the actors perhaps do a bit of audio dialogue for the missions)
I know some of these are probably out of the question. But if even 50% of these could be implemented, the level of immersion would hook a lot more people.
short- make it so you can "refit" a lower tier starship to the next highest tier and so on. Including Bo's slots and stats. This will add alot more variety to the end game and let people keep ship hulls they like, such as discovery etc.
med-add more random and crazy stuff to exploration missions. Weird, exotic, aliens and monsters.
long-more playable races, like romulan, and more character slots of subscribers, 3 is weaksauce!
Not sure if these were mentioned yet, not gonna read 100+ pages
Short Term: Enemies (especially ground) deal 2x current damage. Enemies notice you from further and attack (especially ground.) Takes 2x+ to level.
Mid Term: More dangerous combat, land and space. Much larger galaxy, many more planets. Random/more Random encounters anywhere in space ala enemy ambushes.
Long Term: Large planets to explore. Interactive bridge, player housing on ship/bridge. Zone/block in space uncontrolled where there's a constant battle over control points between factions. CPs could be space stations, planets (ground battles for control)etc.
Fix the z axis for ships, there are several times when something is above you and your ship simply wont point straight up to travel to it.
Set something that is hotkeyable for easier autofire. I don't want to click five different buttons in rotation to get all weapons going. I steer with a mouse so I don't want to "click" on fire all beams, or fire all torps. I like having hotkeys and cooldown timers, but trying to hit control+9 to get a special going is awkward. With some sort of "all fire" button hotkeyed, it could save a lot of room on the 1-0 space for more frequent battle option choices.
Fix dialog errors, ie spelling, grammer, inconcistancies. (There are many)
Crafting. It doesn't exist. Memory alpha is not crafting at all, it is just collecting a bunch of loot drops and trading in for another item. There needs to be a diversity in what is made by different players for it to feel more like crafting. Someone more clever, with more skill points assigned, or who takes more time could have a better result than some one else who just throws it together, for example.
Reverse engineering. This was by far the best element of SWG. Loot drops of the same kind can be added together by a reverse engineer and the best stat from each piece is taken and used on the end result. For example, an engine loot drop has +15 to flight speed and +12 to turn rate and a full impulse speed modifier of +60 another engine loot drop has +10 to flight speed and +16 to turn rate and a full impulse speed modifier of +60 as well, When time is spent researching the drops, it combines the two engines into one with +15 flight speed, +16 turn rate and +60 full impulse. The level of the item would determine how many were needed to research. MK II would need two, MKIII would need three, and so on. If you have an engineer with reverse engineering bonuses, he adds a small percentage increase to the end stats, etc. The items could go into a research depository and game time played would be required to finish researching, so you wouldn't be able to use ANY of the items you put in until it was finished. The greater the level the longer it would take, maybe even as long as a day of playing. Just some thoughts.
Use ships for everything they would be used for. Little mini areas for you to explore other than your bridge. Potential stow aways that need to be dealt with. Sabatoge missions. And most importantly, a CARGO hold. Why should I have to fly to a space station to pick up huge items out of a little bank terminal? I should have it stored on my ship. My characters inventory should be restricted to things my character could actually carry and the ship should have a cargo for more items. A cruiser could hold more than an escort, etc.
Mission diversity. There should be multiple options to any engagement, and your stats should determine the outcome. Stats for negotiating could be added when dealing with a group of romulans or something. If you encounter Remens it could be universal attack from them regardless of negotiation attempts, and certain scenarios will have more "starfleet like" options.
Short: Scrap the Death Penalty idea.
Seriously, you'll probably kill the game if you implement this.
Mid: Complete ship exploration instead of just the Bridge.
For example, it would be pretty great to be able to go to your own ship's Ten-Forward, Engineering, and Captain's Room. This could also open up new ship customization options for players. I enjoy the Bridge and its customization options but it just seems too limited.
Long: New "Boarding Party"-type PvP map(s).
It would be extremely fun to go up against an enemy team with the objective of defending / taking over a ship.