The game:
- massive multiplayer
- 1 vs 1 battles that are auto ressolved (you click a "battle" button and get the result, no tactics)
- text based (combat results presented as text, so there can't be too many rounds of combat and too many unit groups)
- browser based (so I'm quite limited when it comes to hardware and data complexity, definitely I can't simulate and store every single ship as a separate entity, it has to be based on some sort of groups or stacks of units)

More:
The game will be more about designing your fleet and spaceships. The combat alone will be more like getting the fruits of your labour and putting yourself on a test if you did well or not.
The major issue is the representation of the battle. It is all text (with some icons I guess). Therefore I will have to make the units fight as stacks (1 stack groups all spaceships of the same design), I think 8-12 stacks per player max. Also the number of rounds (ships exchnaging fire) should be quite limited, otherwise it will be a wall of text. So the battle should be reasonably short and then some algorithm should determine who was the victor (not a battle to the last unit standing). I'm not sure if there will be permanent loses yet (the ships could repair themselves after the battle), anyway, this is not related to the battle itself too much so we can ignore this.

My idea:
I want to make it simple and easy by using the standard damage-hp system, to not scare new players and make them feel familiar and comfortable. I also want to introduce some cunning advanced things to older players. So I thought of making the majority of the battle a standard "unit X damaged unit Y and dealt Z damage" and toss around several "mysterous" checks. Also, the new players will have rather primitive fleet made mostly of simple damage and kill spaceships without much complex rule changing modules.

Unit/entities types:
- 5 classes of spaceships (battleship, cruiser, destroyer, frigate, corvette), these are grouped into stacks
- fighters (transported on spaceships)
- missiles (launched from spaceships)

Combat rounds:
- precombat checks and bonuses - initiative, morale, sensors, etc
- round 1 - fighters are launched and approach other fighters only
- round 2 - missiles are launched, if you have more than twice surviving fighters than enemy all fighers above the twice get a "missile intercept check"
- round 3 - long range spaceships weapons fire
- round 4 - medium range spaceships weapons fire (the long range weapons fire too, fighters are still fighting as well but at this point probably targetting the spaceships, at this round most spaceships are out of missiles and no new missiles are fired)
- round 5 - short range spaceships weapons fire (all long range weapons get 50% penalty, abordage allowed)
- round 6 - short range spaceships weapons fire (all long range weapons get 50% penalty, abordage allowed)
- end of combat

Generally, the spaceships appoach the other fleet firing lower and lower range weapons as they come closer. They target an enemy stack, fire weapons and deal damage to the stack.

Combat rules:
- fighters attack enemy fighters first, then missiles, then big spaceships, then medium ships, then small ships
- small spaceships (corvettes and frigates) attack enemy fighters first, they also get a bonus vs fighters
- during first rounds weapons target biggest/strongest stacks first, in the last rounds the weakest stacks
- spaceships with "anti missile hull" will attract missiles (much higher chance that missile will target this ship stack), such event is not fortunate to missiles since these ships will have the highest chance of destroying missiles before hit, better missile guidance technology can reduce the chance of this
- if at any round all your fighters are destroyed you get 10% morale penalty till end of battle
- if any of your spaceship stacks is fully eliminated you get 3% morale penalty till end of battle
- before combat all sensors of both fleets are compared (average senors of all your ships (the sum of sensors / number of spaceships) + sensors of your top 10% best sensor ships (to make a specialised sensor units worthwile while not making sensors on average ships irrelevant)), the fleet with better sensors score gets a bonus

Advanced rules (technologies/modules):
- fighter fire control - some of your spaceships can provide this to your fighters, all fighters under it's influence get some bonus. For example a carrier spaceship could hold 20 fighters and provide "Fighter fire control level 1 for 30 fighters; Fighter fire control level 2 for 10 fighters; Fighter fire control level 3 for 5 fighters" (so it can provide it also to some fighters launched from other spaceships since the carrier's bonus capability exceeds number of carried fighters, it can be used to boost fighters carried by a primitive destroyer that does not have any advanced elecronics). So, as the technology progress go you will be getting all fighters covered with the influence of the level 1 bonus and some with level 2, then you probably could get a full coverage of level 2 and will be simply ignoring all modules that grant you level 1 since you don't need it.
- bigger spaceships will provide "Fleet control for X spaceships", if you don't have enough of these you get a penalty (so a proper ratio of big to smaller ships should be kept, of course you could mount such module on smaller ships instead, but not for free)
- shields - some units could generate shields that surround the whole fleet, a portion of damage can be abosrbed by the shield (I wanted to make individual shields but it would make no sense with the stack system)



Comment, or give your ideas related to the topic (I'm just collecting ideas and sorting out thoughts now).

Unless i don't get it, i think it's perfectly fine to store every single ship as a single entity. Databases are very powerful and there is plenty of room for dozens of ships for thousands of players.

Warring Factions used to have 500k ship battles where each ship was a separate entity. Of course it bogged down a quad core server

Fighters in space doesn't even make sense. Save yourself a lot of hassle and remove anything below frigates.