May I interest you in comprehensive ship interior customisation as a means of player housing, NPC crew / security escort uniforms, PvP/PvE boarding action area, episode mission tie-ins and mini-games that earn real rewards?
My dream update would include being able to create client side mods, much like in WoW, being able to customize your ship better (I remember seeing a preview of STO in a gaming magazine a few years ago that showed a saucer section with 'cut-out' pieces), more options for the alien option including tails, muzzles, etc., the ability to customize the color of your energy weapons, and the option to pu the UI down on a second touch screen with a few more control buttons so that you can control the entire game from that touch screen, just like how the computer consoles were controlled in the shows and later movies.
No Dilithium in Crafting. An actually GOOD crafting system that better fits the IP. Hundreds more story missions with good item rewards. Reasons to play more than Di Dailies and STFs at max level. An actual PLOT. A fully-fleshed-out KDF. A good Exploration System. The ability to roll in Space/Dorsal and Ventral Shields. PvP missions with the opprotunity to capture enemy faction starships. Territory Control.
Oh, and better odds on Lockboxes. Right now, the odds are too low to be worth it.