Assuming some weird fate happened and Cryptic Studios/Perfect World called me and said, "Sanford, we want you to head up a new Star Trek Online II project", here's what I would suggest.
Item 1: Make The Game Federation-Only
As much as people would like to play Klingons, Romulans, Borg, Xindi, Cardassians or whatever, there's just not enough material to justify an entire MMO leveling-arc around any of these species. Players can choose to run story-based missions from the other factions ("alt"-ing), but their primary characters should be Federation.
None of the "alt" factions should have any interaction with each other - strictly for story purposes. Lord of the Rings Online has proven that this system can work, and there's no reason to think that it wouldn't work in STO. So therefore, make PvP similar to "Monster Play" as it exists in that game.
Give a few developer-created missions for players, but also allow User-Generated Missions to fill in the gaps.
Item 2: Get Rid Of Instances And Use Focused Servers
As we've seen with the uniforms and ships from every era of Star Trek being in the game, there is a wide and varied enough fan-base to support this idea. Make servers for each "era" of Star Trek, and make the missions, ships and uniforms fit the time period.
One HUGE complaint from players is that there's no reason to have an NX-class ship or an Original Series Constitution flying around in 2409, and even the fact that they're technically "refits" still does not sit well with the player base, and feels a bit like a cop-out explanation.
So, I suggest splitting the game up into different servers, each of which focuses on a particular time period in the Star Trek story.
- Enterprise - NX-class ships, the blue jumpsuit uniforms, and lots of exploration. Players have the option to "alt" as Klingon or Xindi-remnant species as their faction. Obviously, this would be based after the Founding Ceremonies of the Federation in "These Are The Voyages...".
- TOS/TAS - Constitution-style ships and "sweater" (classic) uniforms. Players have the option to "alt" as Klingon or Romulan. This one covers everything after the end of the animated series.
- Original Films - These are the Constitution Refit and Excelsior era ships. "Monster Maroon"-style uniforms. Similar to the TOS/TAS above, players can "alt" as Klingon or Romulan. These take place after the assumed death of Kirk as seen in "Star Trek: Generations".
- TNG/DS9/VOY - Characters can "fill in" the time immediately after the end of Nemesis, following the story as it unfolds in the "Path to 2409", "Needs of the Many", and "Star Trek: Countdown" installments. Everyone is in either the uniforms from the shows or the "Movie" uniforms. Plenty of ships to choose from. Players can "alt" as Klingons, Romulans, or Cardassians.
- "Reboot" era - Using the alternate timeline from the 2009 J.J. Abrams film, make this one similar to the TOS/TAS option listed above, only throw in that Vulcan has been destroyed and make some of the missions revolve around that fact. People wear the updated version of the classic uniforms. "Alts" follow the same path as listed above.
- 2410 (or, "STO Legacy") - Continue with the story arc of the game as it currently stands, for those who enjoy the tales it tells. Limit people to the era-specific uniforms introduced in the game. Players can "alt" as Romulan or Klingon.
Some may think that this will "splinter" the player base too much, but I think that it will make each server feel more alive, since everything will have its own style of play and nothing will look out of place.
Of course the best work-around for this is that a character can be "ported" from server to server, with all of their stats and abilities following along with them. The only thing that changes is their appearance and the availability of missions in whichever server they're currently playing in.
Item 3: Uniforms Must Be Uniform
Another common complaint among the player-base is that while uniform customization is nice to have, the fact that every player is running around with an infinite number of variations on a vast number of uniforms makes the game lose the "Star Trek Feel" that we all wanted when we first started playing. Seeing people in bright green TNG uniforms kinda breaks the character immersion.
I say that every uniform per faction (depending on which server the player joins) should look like something you'd expect to see on the shows of the time period represented. All division colors match those seen in the shows. Leave the customization options for "off duty uniforms" that are worn in social zones.
Item 4: Level Progression Instead of Rank Progression
It's no secret that there are just too many Admirals running around in Star Trek Online. Personally, I think that each player choosing to run a ship should start off with the rank of Captain, and "leveling" is handled in a numeric scale, allowing the Captain to level up exactly how it's done in practically every other MMO.
It makes more sense to tell people you have a level 33 character in a game, than to say "I'm a Lieutenant 3".
The title of Admiral should be reserved for people who run a Fleet -- no exceptions.
Item 5: Not Everyone Wants To Captain A Ship
Maybe I should have put this before Item 4, but it's a good point to make. Some people just want to be healers (Medical Officers) or work in the engine room. Even William Riker was perfectly content as the First Officer of the Enterprise, refusing promotion to command his own ship on multiple occasions.
I say give players the option to be a "ground only" player. Let them choose to work in a Starbase, taking shuttle crafts or runabouts to perform missions. After time, they can be assigned to a ship, and instead of running every space or ground mission, they perform a certain task, and provide a bonus to that ship based on their class.
When I first heard that there was going to be an MMO based on Star Trek, I let loose the loudest "fanboy squee" ever heard. However, once the "newness" of the game wore off, I realized that there were just too many things that didn't feel right about the game. After reading countless reviews and the Official Forums on the STO website, I realized that I was not alone in my opinions.
Now, don't get me wrong -- Cryptic has done some amazing work in bringing the game out of the embarrassment it was at launch, but it just feels like they're trying to shove as many thumbs as they can into the leaking dam. The best way to make Star Trek Online better is to just nuke it and start from scratch.