At this point, fleets are literally just a block of code with a health and dps stat. Whoever has more of these will win. So, why would we ever put frigates or destroyers in our fleets when battleships and cruisers are superior in both health and dps? In real life today frigates, destroyers, corvettes are used for mainly defense. And it should be the same here.
First up, make missiles and torpedoes be the only weapon to bypass shields. All cannons will be stopped by shields. Destroyers and frigates will be used to shoot down enemy missiles torps and fighters, and battleships/cruisers and dreads will be the main offensive ships. Since doing this will make battles much longer, we need more ordnance. I suggest increasing ordnance module supply by 10x, but also bring back the conversion mechanic so that 1 limbalt is equal to 10 ordnance. When under attack by a missile threat, each weapon on the ship will shoot at a different missile. Your medium weapons would engage first, and then smalls. So, an enemy Red Radiance battleship equipped with 2 torps, 4 missiles and 2 small cannons engages one trafalgar destroyer equipped with two missiles and two small cannons. The trafalgar will shoot down two of the missiles with its own medium missiles, and the cannons will shoot down the other two missiles. Now, torpedoes I would prefer to take two shots to shoot down, so if the trafalgars two small cannons reload in time, they would only shoot down one of the RRs torpedoes. One of the RRs torpedoes, and the two cannons will strike the trafalgar but its shields will stop the two cannons. On another hand, a Resolute dreadnought equipped with all six torpedos and two missiles engages a Solaris destroyer, with all eight missiles. The solaris will use two missiles for each of the Resolutes torpedoes, so it will only be able to shoot down four of them. So it will be struck by two torpedoes and the two missiles. This is only 1v1 fights so far, so lets get more complex.
A fleet of 14 trafalgar destroyers, 3 valkyrie battleships and a resolute dreadnought engage a fleet of 13 solaris destroyers and 3 red radiances.
The mankind fleet launches 14 missiles and 12 torpedos. The PR fleet has a total of 104 missiles to defend the RRs. 14 of those missiles will shoot down the 14 mankind missiles, and 24 of those missiles will shoot down the 12 torpedos.
The PR fleet launches its 12 missiles 6 torpedoes and 6 cannon shots. The mankind fleet has 28 missiles and 28 cannons to defend the valkyries and resolute. 12 of those missiles will shoot down the 12 attacking missiles, and another 12 of the missiles will shoot down the six torpedoes, but the six cannon shots will still strike whatever the enemy was targeting, being blocked by shields.
So, this fight will last quite a while, but I feel the PR fleet will win since it has so much more defense than mankind, and the RRs still have cannons which will eventually lower the shields of the mankind fleet. Both of these fleets will need more offensive ships.
What about fighters? I think these should take five missiles to shoot down, since in their animation there are five fighter jets being launched per carrier. I also suggest that all dreads can use all of their slots for fighters like the snake and pr dreads can. With the six slots used for fighters, it will take 30 missiles to shoot them all down.
I think this will fix all the problems of no reason to build t2s or 1s, battles being too short, the inability to protect ships, and lack of engagement when designing fleets. I mean, I see people who get so bored of doing formations that all their fleets are of the default clumped up formation you get when you first form the fleet. Thing i see with most battles is that the dreadnought dies first. That should never be the case.