How about you guys set up a forum were people can write and design missions. This only works if someone is listening. Make it a contest even. Once every other week or month or so, you all select one of them and make it. Judging by what I have seen so far, the game engine has more that enough capability. COH/COV has the mission architect thing, but I don't think STO is far enough along for that.
The only other suggestion I have is to make the missions more personal. Star Trek in general was about the characters. If there were a few missions were say one of your bridge crew was kidnapped and you had to rescue them would be cool (Bridge interaction scene) or the captain was captured and you had to play one of your bridge officers to save him/her. I saw that you will be adding wildlife to some of the missions. Very good idea. There should be more NPCs and wildlife (Hostile/Friendly) in the Nebula/Cluster missions. Adds to the effect. (Remember the new Star Trek movie, Ice Planet + Big Hungary Alien Creature = Fun)
That is my 2 cents. Other than that, The game is superb and can only get better from here. Keep going guys...
Summary: A planet is being bombarded with meteor showers that are decimating the planet. You and your crew must beam down to multiple sites and set up shield generators
Beam down to multiple points on a single planet in multiple terrains. In each terrain, you must set up a shield generator. Some environments are friendly, some are hostile (wildlife mostly).
Terrains & Weather patterns
1. Hostile Aliens
2. Hostile Wildlife
3. Harsh Weather
4. Meteor Showers (Potential Damage)
5. Small Town (Friendly)
6. Small Town (Hostile)
Also Kirk, Picard, and Crews saved earth a bunch of times. When is our turn to do that. I am not saying we need a whale probe, but something equally cataclysmic would be cool. or maybe a earth based fleet action!
I mean, This game currently has the single greatest concentration of Trek lovin' people next to your average Trek convention. You have to figure that there is also a large number of them who could come up with some amazing missions. The game engine can handle it. They are a untapped resource. (Free resource if cryptic played their cards right) and I bet they would jump off a cliff to see their mission idea become a reality. We just need a conduit to do it. (Hint, Cryptic, Hint)
Fleet Actions Assault on Starbase
A fleet action to take over a starbase. Basically Starbase 24 in reverse. (maybe Starbase 24 on the Klingon side? Alternatively, an attack on Deep Space K-7 for Klingons?)
Exploration Missions Aid a planetary Investigation
A mission where you aid a local government in finding a particularly elusive criminal. Might be due to a difficult political situation, or due to a unusual type of enemy (Changling or Undine, most likely). Talk to some NPCs and scan some blinkies. Once you have identifed the criminal, you might have to fight him.
You beam down to a planet to do some exploration and a monster attacks you. The monster might retreat instead of die when you "kill" it, and return later.
For Klingons, your goal might be to hunt the monster and keep it as a trophy. (As a special, it might drop some kind of anomaly material instead of the usual.)
The mission might otherwise be just one of the usual "scan 5 objects" missions, but instead of fighting normal enemies, you fight a unusual monster.
Hunt a Cloaked Raider
Some is attacking freighters in the area. It must be a cloaked ship. You have to scan multiple areas or escort a freighter, The enemy ship might decloak a few times and attack you, but retreat and cloak before you can take it down (e.g. instead of a "kill animation" you get a "cloak-animation") for good. (Maybe your Science Officer tells you they have found a way to disable its cloak.)