A combat system of most long term non-FPS games (those that take days to play out, MMO's are considered as long term) tend to lack the ability to allow the underdog from defeating the powerful opponent.  Although throughout history there have been numerous cases in which an outnumbered and out-gunned group defeated a much superior force, even with conventional warfare tactics.  This goes far back into the ancient times, a single Roman Centurion defending a bridge in Rome against the Barbarian Hordes. 

For a game that is to be a MMORPG (with emphasis to the RP), the combat system would need to be done in such a way where players do have the ability to become heroes, where their own skill takes some form of the action, be it in terms of physical agility of the hands and fingers or of the mind.  Equipment, vehicles, ships and their technology only serve as an advantage, not the deciding factor.  It is the human element that is the critical item, and this element should have even more focus for players of a RPG.

Now I'm not saying that poorly commanded large capitol ships will always loose against highly skilled frigates.  There are other factors at work:
- The Elements (Nebulae, Asteroids, Suns, Gravity Wells, etc)
- State of condition of the ship's systems
- Possible mishaps
- Fog of War
- Luck

However even with such factors involved, battles in the computer game environment often do not mirror what occurs in real life.  Often the batters are either fought to the death or on and on until one side gets tired and quits for the day.  Such tactics are similar to old Russian tactics, unorganized mass assaults without regard to casualties.  Since after all, there is very little to loose as the death penalties in such games are light.  In a sense the meaning of battle looses its point or objective.

For example, The Naval Battle of Samar (link below) provides an example of the type of combat I would like to see made possible.  Not that this would always happen, but that the possibility would exist.  In brief, the Battle of Samar was part of the Battle of Leyte Gulf (WW2), in which a superior Japanese Battleship Group engaged a light US Escort Carrier Group.  The Japanese had gained surprised and were able to engage the Escort Carriers at gun range.  As the forces drew near, US Destroyers and Destroyer Escorts charged against Japanese Cruisers, Heavy Cruisers and Battleships.  The US ships were outnumbered and out gunned (5" guns compared to 8", 14" and 18"), but did have torpedoes.  However they would have to get within 5 miles to do so...  5 miles is close considering the 18" guns could hit out to 25 miles.  Then factor in that the armor of Destroyers are considered paper-thin compared to Cruisers and Battleships.

One particular Destroyer Escort, USS Samuel B. Roberts, engaged at ranges in which 20mm cannons were used, and the large caliber cannons of the cruisers could not be used, for either elevation purposes or risking damaging other friendly ships.  This action would earn the Roberts as “the destroyer escort that fought like a battleship.”

Although there were about 400 US aircraft involved during the fight (from the escort carriers), the heroic actions of the small ships should not be dismissed.  By their actions they were able to hold off the Japanese Force from sinking all of the carriers and eventually bought enough time that the Japanese Force would retire for fear of a counter attack by another US Fleet.


Battle off Samar (Wikipedia)
Link:
http://en.wikipedia.org/wiki/Battle_off_Samar

Should such a scenario occur in a typical MMORPG setting, the result would be the victory for the Japanese as the Japanese players would press their attack, since they have the superior ships and need not worry about what happens after the fight.  The US players would most likely retreat as a Destroyer has not chance of taking down a Heavy Cruiser.  For example a Level 25 Ship going head to head against a Level 50 ship, just doesn't work out by the numbers for the Destroyer.  But in real life, even a Destroyer could sink a Battleship (by the use of torpedoes, still no easy feat).  There is no fear for one in loosing a fight other than perhaps of some lootable item or delay in time. 

So what other factors or rules could be applied?

Then again assuming that such a style of combat is something that players would like to experience.

That is good to know.  But by saying, "ship combat will be Bridge Commander esque," does this mean via controls and interface or by how the combat system will work?

   Actually what he said was that combat would be more like "tall ships" requiring manuvers and timing to defeat an enemy.  But I agree with you, combat should be decided by skill rather than who has the biggest and more numerous guns. But knowing the typical mentality of "most", brainless pvpers if such a system were implemented, they will scream and whine that its too hard and demand cryptic to dumb it down for them.
  I personally would really like to see a game that for once espouses using your head and creative tactics.   Another really good example of this kind of play was demonstrated in the TOS episode "Balance of Terror" as well as in the movie "Wrath of Kahn".

You made a good point with FPS games which I liked in to finish a mission or win over a final enemy. Therefor I found multiplayer games not alike generaly MMORPGs.

A viewscreen for the fight of a enemyship under fire should fit in. I'd like to have RR inside my ship with my crew joined forces with Klingons, Romulans & all the friendly species Federation or not.