-Above all, first and foremost, and drop everything until it is done and done right; Fix science. Seriously, how could you have let this go on this long? Inexcusable. You only have three playable professions in this game and you've removed one from viability entirely. Fix it.
-Fix crafting. The current status of crafting in this game is a shameful, shameful stain. Seriously, breaking in game crafting so you can profit on the cstore? Are you serious? How shabby is that?
-Overhaul PvP or remove it from the game. Gozer is working on this I'm told. We'll see.
-Remove the respec token cost. This is just sickening to me. You have routinely broken the skill system so often that charging people to respec is starting to look like you're breaking the systems on purpose. Given the direction your corporate model has taken, this wouldn't shock me. Basing the game on having multiple ships, and then making all of the ships so crippled they require their own spec to pilot effectively is inexcusable. Either fix the skill system or remove the cost of respeccing.
-Fix the Dread. Not add that stupid saucer console, ****ing fix it and make it perform as advertised. Rearrange the eng and tac slots and make it a ****** warship, not a ****** exploration cruiser. I know cryptic is historically nerfhappy, but this was ridiculous.
-Remove the time gating from the shuttle event. I know you are having difficulty putting out quality content, but gating it so no one can participate in it is EXACTLY THE SAME AS IT NOT EXISTING.
-Put out a new strike force monthly and add it to the pitiful rotation. Focus on the Romulans or the Borg rebellion. If you need help I will write it for you. (both of which really, really should have been a playable faction by now)
-Fix the Crystalline Entity encounter. That is unacceptable.
-Implement branching storylines. Again, this game has almost zero replayability. There is no content. Add branching possibilities to each of the existing missions, three in each scenario. Each option will have a unique element that changes the next encounter accordingly and so on.
-Repair the Klingon faction. As in bring it's content up to date, provide costuming options for both PCs and ships, you know, all the things that should have been done when they were introduced. As it stands, the Klingon faction is broken and incomplete. Finish it.
-FIND A DIRECTION TO STEER THE GAME'S CANON. This is getting to be absurd. I play this game because I want to play Star Trek, NOT BATTLESTAR GALACTICA. Star Trek is historically about new life and new civilizations. There are some incredible suggestions for just that sort of thing on this board, three or four come to mind in the space of about five seconds, none of which would require much in the way of new technology or resources. Focus on exploration, meeting new cultures and creatures. Don't half *** it either.
-Expand the zone limitations. HOW CAN DEEP SPACE BE CROWDED? Expand the zones to three to four times their current size or remove the zone walls altogether.
-Create a checkbox for Random Encounters Yes/No. As you travel in space, you get the idea. Distress Calls, anomalies, etc. Use your imagination.
-Make a clear distinction for the Cstore purchased ships. If a ship has been purchased from the Cstore, don't break it to make your new bait and switch or lockbox scam shiny seem more attractive. That establishes a very, very bad precedent.
-Complete class system overhaul. Having only three enormously broad categories at character generation is one of the chief things that cripples replayability for this game. You have nearly sixty years of canon to work from. It's not as difficult as it sounds, and it's not like there's a dearth of material to base it on.
-Introduce both the Delta and Gamma quadrants, each in their own season. For obvious reasons, as in seven years of the IP's canon took place in each of them. Seriously. Where are they>?
-Expand the political aspects of the game. The Star Trek universe is teeming with factions, unaligned worlds, strange entities and whatnot. Where are they? The interplay in all of this is the reason there was a Federation. Seems like kind of an important aspect of the IP to just ignore it completely...
Really, this would put you in good stead for two or three years at least.