I have messed around with the game for a while now and I have found that there is a really large issue with the way combat plays out as ship sizes increase.
-- Weapons generate more flux than they deal damage --
Unfortunately it is true. Take a ship with a 0.6 flux/damage ratio on its shield. Let's take a standard beam weapon attacking it. 1.0 ratio on flux/damage on firing. This means that for every 60 flux you create on their ship you create 100 flux on your own. If you take into account the maximum bonus damage from high flux on energy weapons, this still only reaches 90 flux on their ship for 100 on yours. As a result I have actually found it easier to fight another large ship by turning my shields off except for stopping missiles and using my armour to take their shots while returning with maximum firepower. This overloads their ship quickly, and you can return twice as much damage while they are overloaded. Ballistic weapons are no different really, while they do convert your flux into more flux on their ship is does also mean you have to hit them to begin with. A few missed shots leave them no better.
Summary: Increase the damage/reduce the flux of weapons
-- Missiles are excessively efficient/Armour is deficient --
Missiles are brilliant put simply. Brilliant to the point of being overpowered. Using a couple of Harpoon launchers you can reduce a ship with full armour and no shields down to the verge of exploding with a full volley. There may not seem to be an issue there, and really there wouldn't be for smaller ships, but for Cruisers and Capital Ships this is hell. Take 2 frigates with 2 Harpoon launchers each, fighting a large ship. These ships can take turns harassing with their weapons, venting flux when the other one attacks, leaving themselves in no danger. Permanent flux will build up on the large ship though and eventually it will need to drop its shield or overload. Once this happens, a full volley from each ship and the large ship is done for. 2 cheap frigates just took down a large ship quite easily. Missiles wreak havoc on anything without a shield. Once a large ship loses its shield, it is done for, because it cannot maneuver out of it, and point defence can't deal with volleys. Point defence and armour needs to made viable to counteract missiles. A Capital ship without its shield should beat a cruiser with its shield 9 times out of 10, but armour is not a viable defence.
Summary: Large ships should have more significant armour or better defences against missiles.
-- Large ships are too slow --
No offence, but the cruisers are way too slow. Large ships should not sacrifice that much speed on their smaller counterparts. Their maneuverability is as bad as it should be, it is spot on, but large ships have no chance of catching a small ship even if they are in the right position. Large ships should probably have around 75% of the base speed of a small ship. Think of shopping trolleys, one filled, one empty. They can both move with speed, the filled one probably slightly slower, one just accelerates slower, and takes more time to slow down. Other than that, the filled one cannot turn a corner if you wanted to. (Half filled ones drift like a dream though)
Additionally, once you reach that top speed, who wouldn't have fun ramming that into another ship? With that much momentum it could actually be a viable tactic.
Summary: Increase the base speed of most large ships
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Currently, battles between large ships are just resolved by which ship can better cope with its flux. Because attack and defence are no different both ships essentially gain the same flux before the one with lesser ability to deal with it collapses. Some ships need to be able to get by without shields, and better weapon usage should result in the other ship receiving more flux. Permanent flux damage does not solve this, as once a large ship commits to the fight, the fight is to the death. These changes would increase the focus into position to get maximum effect, and add more depth to combat.
tl;dr:
- Increase the damage/reduce the flux of weapons
- Large ships should have more significant armour or better defences against missiles.
- Increase the base speed of most large ships
These are just my thoughts on combat, thanks for reading them. I hope it all makes sense as to why I would suggest these methods.