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So basically as you progress through the tech tree you just build larger and larger ships, there's absolutely not point in having smaller ones. It is always better to have one ship with 200DPM and 200HP than to have 2 ships with 100DPM and 100HP each because:
1. One of the smaller ships will be destroyed first and there will be one less gun firing.
2. Certain modules like Warp Drive and Command Center do not scale with the ship size. The same warp drive will take a dreadnought and an escort to the same warp speed while taking up the same room on each ship, therefore it is always more efficient to build bigger ships. In the end, it is really dump that for ship design you just stuff everything in and destroy an entire fleet with one ship.

Solutions:
1. Since this game does not support module scaling like some other games, a way to do it is to either force the player to add multiple warp drives into one ship, or just make the warp drive less and less energy efficient with increasing ship size. So it will eventually come to a stage that a dreadnought is totally incapable of high warp travel not matter how much energy cores you squeeze into it.
2. Ships exceeding certain sizes cannot be built by normal stations, and they cannot dock on normal stations neither, making repairs/retrofit work difficult. You need to build a special station exceeding certain size to do so.
3. Bigger ships have more difficulty in staying stealth or avoiding fire. Clocking device and ECM generally dont work well on dreadnought class ships.

EDIT: Also changing the variety of weapons can help to make smaller faster ships useful. For example, phaser array can fire 360 degrees and has longer range, however it is bigger and less energy efficient, therefore it is only good for big slow ships. Phaser cannon can only fire forward, and has much less range but a lot more energy efficient, so you can build some fast raider ships that are good at hit-and-run.

Of course bigger ships should also suffer from mobility punishment, that they are always slower for acceleration and turning, and that cool down times should be added for warp drive. When you warp into a system, you should have a cool down time for like half a minute before warping again, so that you really have to rely on thruster.

How about a ramping superstructure cost/materials that grows with the ship size?

Maybe for each tech, the materials needed to build all ships changes to reflect better building techniques.

The quantity of materials and cost for the superstructure would ramp up as the size of the ship grew.

I like building big ships, but they should take a lot of materials and a lot of construction credits.

I think it can be fixed by tweeking components size like engines, reactors, hab modules/life support etc, so that the impact of building a big ship make them even slower. Weapons speed vs engine trust should be considered in the equation as a small ship should avoid more hits and a big ship should take em all in the face like a boss. Its hard to get to a perfect spot currently it seem.

Also energy(ei:fuel) used should be an even bigger issue for mass Big Ships users but currently its hard to balance out, cuz if you have a good economy going you tend to not have fuel problems at all...maybe if fuel would be more rare in the galaxy it would make smaller design more efficient as they would be more gas efficient and can be split to multiple group at a moment notice to get more missions done at any given time.

Anyway for my part I made it so that my construction size limit is fix at 1000 right at the begining(for now,I,m testing it) and construction tech only serve to enhance construction speed. I think it might be the best of both worlds for me for now. I think that ressources/money is the only limit in construction size in our world atm, if we had the will/funds/ressources we could probably start to make a space station as big as the moon if we wanted lol. So thats my reasoning

Even if you have 1000 size limir doesnt mean you want all ships that big anyway, smaller design are still useful and faster to build too. Only very small military ships are completely useless atm.

There is one reason to have 2 small ships instead of one big ship: One ship cannot be in two locations at the same time, two ships can.

I am a big fan of large, slow indestructible weapon-bristling battleships, but I do have my share of small, fast ships. Just to be able to be in more places simultanously.

I have always been a proponent of fleet actions over solo. Yet DW doesn't really support fleets in a fashion similar to typical Naval fashion.

Take something for example like a USN Carrier Strike Group's core, 1 Carrier, 1-2 Helicopter Carriers, 1-2 Anti-Sub/Surface missile ships, 1-2 Guided missile ships. Then add as needed more of the previous, AEGIS ship(s), resupply, etc...

See for examples - Strike Group Photo

Meanwhile in DW I commonly devolve to 3 Maximum Hull sized units, Carrier, Battleship and Bombardment ship. Mix those unit types as needed. No need at all for smaller escort ships.

Actually, one MASSIVE thing the Devs could do to make fleets viable is add a rule to make fleets travel as a unit. Currently if I were to mix Carriers, Cruisers and Destroyers in any long distance travel they will be spread out over half the travel path and arrive singly. What point is their to combined arms actions when the Escorts arrive and die days before the accompanying Big Guns arrive?

Very easy to fix (from a human player stand point, not sure about the ai), have a surcharge on either individual components, or components thresholds.

So keeping existing costings, and add:

1. A 1 component ship adds +1 to cost, two competent ship +2 to cost etc, etc

2. Ship over 300 components have a + X amount cost, ships over 500 components have a + 2X amount cost.

The above it just and example, the rate, scaling and so forth could be easily tweaked for balance, but the end result should mean one large ship will be much more expensive to build and maintain then five smaller ones (with the exact same components, just spread out more).

Edit: Thought a bit more about this, and IMHO it should be a law similar to diminishing returns, where the costs go up exponentially. Aimed at VERY large ships being a special commodity, (ie a large civilization might be able to afford 3-4 of these things, and the loss of which should be a major catastrophe. (Admittedly I am coming from a star trek stand point, where ships take a few years to build, not coming of the production line like hot cakes-a separate issue that I have modded for in my own games)