Here's a list of pros and cons for both games that I wrote up awhile back.
Klingon Academy
Pros:
- Ginsu effect (where you hit the starship, there's a nice explosion, some debris flies off and bang; hole in the hull) looks IMO much more impressive than the damage in BC. While it is probably a bit overdone (ships looking 5x worse than the Enterprise after ST6 can still repair themselves and fight once more) it still looks much more impressive than the damage effects in BC, which usually wind up being far too underdone.
- The environment looks much prettier. The planets, nebulae, backgrounds, all look much better than in BC, with the exception of the stars. Maybe not as realistic, but it's sure as hell more impressive.
- Weapons you are not directly controlling will automatically target and fire on enemy ships that come into range. This can be disabled if desired.
- The music is much more stirring... pumps you up for battle.
- Damage control and power allocation are much more detailed.
- Shields have numerical as well as graphical indicators, letting you know just how much more punishment your shields in a particular area will take.
- Specific shield arcs can be reinforced.
- Ships can be boarded and captured. They can also be defended from capture.
- Your crew can take casualties, and your sickbay can heal the wounded. (but not the dead)
- You can use ECM, and you can pump up power to the sensors to defeat ECM.
- Torpedo tubes can fire off axis. This is a biggie.
- Destroyed ships/stations take a while to fully explode.
- Despite the difficulties imposed by the Ginsu effect, KA has dozens of ship models and classes.
- Quick Battle groups friendly and enemy forces together and separates them beyond weapons range. However, each side is limited to 8 ships. (unless you use a mod...)
Cons:
- Ginsu effect requires significant amount of work to be implemented in any new ship. Ginsu can be ignored if desired, but it doesn't look nearly as spectacular compared to other ships then.
- Ships are far too nimble, and move like slow fighters.
- Torpedos have no tracking whatsoever.
- Short weapons ranges force close-in fighting.
- Starbases/stations are far too small.
- Manuevering worsens with reduced speed.
- Interplay could not make a good Excelsior model if their lives depended on it.
Bridge Commander
Pros:
- Exterior camera tracks target, allowing a superior view of your foe.
- Manuevering improves with reduced speed, allowing for tighter turns.
- Damage effect shows scarring to the hull (as in the ST6 burn marks) and eventually a hull breach which gradually grows larger.
- Damage effect is much easier to apply to BC ships; your computer will automatically generate and use the voxel files needed.
- Phasers deal more damage than their KA counterparts, at least at close range.
- Greater range; range is mostly limited only by phaser effectiveness or torpedo accuracy, as at longer ranges the enemy can more easily dodge torpedos.
- Torpedos track their targets for four seconds.
- Destroyed ships/stations take a while to fully explode.
- Space stations/Starbases are finally as big as they should be.
- Bridge officers can be instructed to continue combat while you attend to other matters.
- In-system BC stars look prettier than in-system KA stars.
- 3D map of immediate area is very useful, though one wishes for the tactical display shown in ST2.
- Nice bridges.
Cons:
- Damage effect is usually underdone; it's entirely possible to kill an enemy ship and not once breach his hull.
- Your targeting system allows only one target to be tracked and fired upon at a time, allowing multiple smaller and weaker ships to have a big advantage over a bigger, more powerful starship.
- Torpedos cannot fire off-axis. That they would design this game with capital starship combat in mind, and then make it so that you had to line up a 640 meter long ship into a firing solution is utterly incomprehensible.
- Torpedos take far too long to reload and do not do enough damage for their long reload time.
- Far too few starship classes, and in my opinion this is really inexcusable considering the vast number of starships we saw in Klingon Academy. How many times did we see an Excelsior class in TNG? Much more than the Ambassador, that's for sure.
- Quick Battle just dumps the ships in a ridiculous big mix. But, the number of ships in said mix is limited only by your hardware.
- Issuing orders to wingmen is clunky and slow.
- Game was balanced (ship stats fucked, etc.) despite interview promises to the contrary.
- Shields have a vague color-code strength indicator.
- The 'simulation' lacks the detail of Klingon Academy, in that power allocation and damage control is severely oversimplified, and shield arc reinforcement is nonexistant. Simplification I can handle, but outright removing the ability to reinforce a particular shield arc is again damn near inexcuseable.