Well, my ideal Star Trek game would have a properly organized fleet; with 'lesser' ship classes having their own roles and specializations, rather than just being inferior mini versions of other ships. It would also have a more unified look than the one in STO; with ships reusing design elements from other vessels (as is traditional in Star Trek).
I'd introduce a strategy game element to ground battles. If I know there are, say, 30 stonking big Gorn on a planet, why would I only send 5 people? I have security teams twiddling their thumbs back on the ship; why wouldn't I send some of them down too?
There would be plenty of missions set inside the ship; a decent number of which would revolve around specific, named, crew members (often the senior staff). These would be optional, so that the player controls how much crew drama they have to put up with.
There would be more to do when discovering a strange new world; maybe something like the scanning mini-game from mass effect 2, which could uncover points of interest which may or may not merit further investigation.
Orion males showing up to battle, without so much as a shirt on, would fall over if shot with a phaser once.
There would be almost as many ways to avoid a fight as there are to get into one.
My decisions would have consequences that would follow me through the game.
Catian characters would have hair options (who even cares about those ones from the films? The only notable thing about them is that they made the species official).
I would include ship kitbashing; but more in the manner of being able to make ships using bits of completely different ships (say, being able to put Ambassador nacelles on a Nebula for example).
The game would begin and end with the player holding the rank of Captain (being a starship Captain is the dream isn't it? The only main character, who continued to be a main character after hitting Admiral, was Kirk; and he hated it).
I would say that it would be whatever makes a good game in the first place. For instance, Armada was a great strategy game. Games like A Final Unity were great classic mystery-solving game.
STO is certainly the all-around best Star Trek game ever made, but it certainly is missing a lot of the elements that have made other Star Trek games great. Specifically, it would be nice to see some real mystery-solving, puzzle solving episodes with voice acting like A Final Unity as well as some real-time strategy, inter-faction resource control games like Armada integrated into STO.
its hard to keep people interested in games these days, especially with a newer, shinier mmo that appears every couple of months.
what some of the more established mmos that have history outside of a computer is that there is a fan base that was established long before the notion of massively, online and gaming were conceptualized.
on a personal note, foundry really intrigues me. i might just start paying the monthly fee just to tweak it (my development side kicks in once in awhile).
I like the idea of starting as captain and ending as captain, but the idea of more "strategic" play as in Armada is also nice. Maybe you start out as a commander, take over your Miranda and are so impressive that SF promotes you to capt. (giving a Lt. command of a ship is only realistic in an emergency, there's no way admiralty would let you keep it). So you go on as a captain gaining something similar to grade that you can trade for ships (similar to SFC) or you can save up some huge amount and "buy" yourself an admiral promotion. With the promotion you no longer fight directly, instead you issue orders to a handful of ships or an away team. Your avatar is no longer involved in the battles. Players can choose to stay capt. or admiral (just like Kirk). You can even take a demotion back to Captain, but then you lose any BOs you have promoted beyond commander.
All Trek games have had very good pieces of the puzzle, they just always stink because no single game has had them all.
SFC: become captain early on and use earned reputation to upgrade ships or (if you choose to play the admiral) buy more ships.
Armada: strategy, this one would only help if you play an admiral, but no run n gun, you have to choose where to place your units. Let's say you're invading a mining complex, beam several teams into different locations spreading yourself thin but flanking or beam all your teams into one location to storm the castle.
In space you fly your command ship and issue orders to the ships you purchased for your captain BO's. You have no control over the powers they use, but you do outfit the ships and they have captain abilities based on career.
I also miss boarding ships and actually taking them. That was always my favorite part of both SFC and Armada, of course that can't be done in pvp but in pve every ship you take could earn extra rewards at the end of the mission.
Unfortunately I never played the Voyager fps so I can't say if it had anything useful. Probably good stuff if you choose to stay captain and participate directly in combat.
A nice bonus would be to start boarding operations in mid-combat (pve) If you get a ships shields down, you can beam over and have a certain amount of time to cross a few decks to the bridge. If you manage it (no easy task, say 3 minutes for 3 decks) the ship begins fighting for you if you fail, your ship pulls you back and you pick up the space engagement where you left off. This works both ways, you ship can be boarded and you are dragged into a defend the ship mission where you have to remove enemy groups from your ship during the time limit before they place charges (blowing up the ship).