Short: General bug fixing. The game's been getting a lot better with this but I'm still noticing stuff like ships being named the wrong class in Klingon PvE missions and my personal least favorite thing in game, the bugs in the Hunting the Hunted episode that keep your bridge officers from following you through the transporters and make the mission nearly impossible to complete. A little bit of polish will make things much better, especially for the Klingon side.
Medium: I rarely play my Klingon toon but let's go ahead and give them some more content. The decision to flesh out the KDF with PvE content is recent and some of the Klingon players have been a little less than reasonable in the way they've been clamoring for attention, but the fact is, if the KDF is going to be a full faction, it needs some work. Right now it's unpolished and a bit empty. Bug fixes, typo corrections, more customization options and a few more ships and well written missions would go a long way toward keeping the existing KDF players content and would make it worthwhile for the curious to try a KDF character.
Long: Just more! This game has the potential to expand off into the Universe in so many ways. Customization options like assigning specific positions to bridge officers, such as First Officer and Chief Engineer, maybe even the ability to assign officers to specific stations on the bridge, I could even see in the long run something like customizable bridges where you start with a basic template and can then choose your own bridge stations & chairs. I'd like to see the uniform template idea that's been discussed so unnamed NPC crew members wear your own uniforms. I expect to see more well written episodes in the vein of the new weeklies and some of the Cardassian space missions that stand out to me as some of the better written ones. Star Trek has so many possibilities beyond just combat and I feel like there is an effort being made to make things more thought-provoking and interesting and would love to see where this goes.
Short term -
Make the Mirror Universe skins available for ships. I like purple and the purple warp nacelles rather than blue would be nice. Darker hulls and Imperial Seal rather than the UFP or Fleet symbol would be nice too.
Have the Canon lawyers forbid the Neural Parasites from the "Conspiracy" story line from being expanded on? I know that they never expanded on it due to the massive negative feedback from Trek fans, so is this in effect for STO? It would be a nice story arc for an invasion. Could be fun.
Getting rid of some of the sillier spelling mistakes, and graphical mistakes.. (for example when my toon beams back to the ship, the part of her collar where the rank insignia turns black for no reason, it's also noticeable on the NPC's at the same time).
Being able to see what the 'episodes' (read quests), will award you from the episode list. Nothing worse than getting a quest for a nice piece of tech, and then mis-remembering which quest it was that'll award it, because the write-ups in the Episode List don't show the rewards for that episode, likewise for quests that award Diplomacy XP..
Adding more traders that sell tech for energy credits (I don't mind if it's in the Captain's Table)... I was miffed that you can't buy anything over Mk2 with energy credits.
Secondary, More NON-C Store female uniform/clothing options would be nice.