On average, there's far,far fewer Star Trek games than Star Wars. But ST games have also been very hit or miss. Hey, I still have that ancient Starship Creator from way back when. Makes a wonderful coaster still.
Anyways, on the PC, the best ST games I've played:
Starfleet Command (SFC) Series: Great series of games that tried to give the management of a starship in combat. You had to worry about how you setup your ship's equipment, officers, and subsystems while underway, and of course combat. The system management was deep, especially with SFC 1 & 2. Your warp core could provide so much power, and you had to prioritize which systems got a % of that power. Impulse, Tractors, Sensors, Shields, Weapons (every weapon sucked energy away), ECM / Jamming, etc. SFC 3 slimmed down on stuff to worry about. SFC 1 & 2 were focused on the TMP era of Kirk. SFC 3 was TNG / DS9 / VOY era. It's been years since SFC 3 came out with little to nothing mentioned about a sequel. But the mod community has been pretty kind to this. Getting SFC3 can be pricey these days. SFC Files
Star Trek Bridge Commander: Made by the guys who did Lucasarts' famed "X-Wing" series (Totally Games). The hook of the game is to play it as the captain, issuing orders to your bridge officers. The "vanilla" version of the game, especially at release, is buggy, but got some decent patching. However, this is one of those games that the mod community has been faithful to, updating and expanding it far from what was originally made. Bridge Commander Files
Star Trek Birth of the Federation: Overall it was average, IMO. Decent game that I did buy. Nothing spectacular or innovating as far as gameplay goes, but you did get the chance to play as the Federation, Cardassian, Klingon, or Romulan factions. 2 things stood out in my mind with this game:
1) Cloaked Fleets of Romulan or Klingon ships ROCK. That initial onslaught, coming out of cloak could win the battle for you right away. A dozen or so Romulan Warbirds decloaking and unleashing plasma torps + disruptor fire can wipe anything out. Cloaks are so great in the game that the campaign is EASY with the Klingons or Romulans.
2) Random encounters & special events: Things like minor races from the shows are discovered. Up to you to decide on what to do with them (if Klingon, kill them, of course). Best of all, powerful entities pop up causing having. Crystalline Entity and Doomsday Machine come to mind. And the Borg of course, with a cube wiping out fleets of ships. These powerful entities could wipe out a population of a planet if not stopped.
As far as the TNG and later series go, TNG got alot of love and attention in games. Voyager, IMO the worst of all the newer series (well, I didn't watch Enterprise), actually had a game or two, while DS9 has gotten very, very little attention, despite the AWESOME Dominion War background in its later years, and despite the series actually being around before Voyager and having more seasons. Enterprise came out but at a time when ST games really slowed down.
Yes cloaking is very OP but there is other balancing factors here, one thing is there ships have no hp u can usually beat them if u survive the first round and yes thats hard if there is a lot of cloaking but u have to get a lot of cloaking and its hard to do that. like Klingon can get 2 times amount of ships for there pop so there fleet being a lot bigger than roms(btw they only got 2 ships that can cloak there most powerful Klingon ships cannot. feringi who u forgot to mention can buy there ships super quick bc they are rich and their food is best in the game so they can get more industry+ they have the fastest ships. the feds have insane research so their quality of ships are really good really early. and caards have the best industry in game to build ships and their ships have insane amounts of hp instead of the high shield count which enable u to survive the initial onslaught.
i guess what im saying if ur really good at botf (including micro'ing ur research so u dont have have to lose half of ur research points when it get 100%, expanding before upgrading to much, etc.) u can stand up against cloaking at least early game and if u do it well enough they cant ever harm u.
btw i feel for a balanced multi-player game u need to have no minor races and random events off. less bugs that way(do to minor race issues).