I had an idea that related to the weapon mechanics fix (
http://starmadedock.net/threads/cannon-beam-rebalance-vs-missiles-realism-coooool.7214/), that would make armor more effective, and as I was iterating on that idea I came up with an idea that would make give smaller ships an advantage at least defensively. That is, nerfing shield capacity and regeneration based on surface area.
The idea is that right now shields act as a barrier that completely encompasses the surface area of the ship, and as the ship gets bigger that surface area increases at an exponential rate. Because of this I think shields should in general have exponentially-increasing power costs on larger ships because they would have to protect a larger area. In other words, the larger the ship, the more shield generators and capacitors you would need to power a shield compared to a smaller ship with less R/C blocks for roughly the same effectiveness.
There are two aspects to this concept - shield capacity and shield power. Right now shield caps create a pool of shield hitpoints that absorbs incoming damage. However, I think that the actual capacity of the shield should be the pool of shield capacity divided by the external surface area of the ship.
To make this simple to visualize, were going to assume our ships are Borg cubes, simple deathblocks of a given dimension. Now assume we have a Borg cube that is 10x10x10 in its XYZ dimensions. Since it is a cube, the surface area is equal to the sum of the area of its 6 square sides, each of which are its length to the power of 2. In other words:
SA(cube) = 6x^2
Based on this, our size 10 Borg cube has a surface area of 600 [6(10)^2 = 6*100]. Now enter a larger Borg cube with a size of 50. It's surface area would be 15000 [6(50)^2 = 6*2500]. Out of the 1000 blocks on the size 10 cube (V=10^3 = 1000), exactly 250 (25%) are shield capacitor blocks. We'll ignore adjacent block bonuses and say shield cap is 100hp/block, so the size-10 cube has a total shield cap of 25000 (250*100). ,Likewise, the size 50 cube has a volume of 125,000 with the same percentage of shield cap blocks per total mass, in this case 25% of 125,000 or 31,250, with a total shield HP of 3,125,000.
As you can see, if the same ratio of blocks are kept, by increasing the size of the second cube by a factor of 5 we've increased the shield capacity by a factor of 5^3 or 125. Both shield amounts are roughly average for that size of ship.
However, now lets say our total shield capacity is spread out among the surface area to be shielded. The size 10 cube has a total shield capacity of 25k; divide this by the SA of 600 and you end up with a shield cap of 41. The size 50 cube with 3.1m shields would end up with 208 (3,125,000/15,000). Obviously these are both crappy amounts, so a system like this would also need a buff to how much shield cap each individual block provides, but I digress. The point is that, the ship that is 5x bigger now only has 4x the shields of its smaller cousin.
Basically, dividing shield cap by surface area would make it so that as a ship's size increases, the effectiveness of shield blocks would decrease, and the ship would have to compensate through the use of an escalating amount of shield cap blocks. Of course, most ships are built more aerodynamic than Borg cubes and therefore would not suffer as much of a difference, but this makes smaller ships inherently tougher by making them easier to shield, and it also makes sense in realism terms.
Likewise, shield regeneration should also escalate relative to surface area. However, rather than nerfing the amount of shield that each individual block regenerates, instead we should increase the power required to generate that additional energy by the surface area of the ship, because the larger the shield the more power it will take to restore shield energy. In keeping with the idea that the shield's capacity is being spread out amongst the ship's surface area, we'll say each point of shield regeneration costs 1 unit of ship power for every 10 block surfaces being shielded - therefore, a cube shaped ship with a shield regen of 250hp/s and a dimension of 10 would cost 15k power per second (250*600/10 = 250*60), while a cube ship of size 20 with a shield regen of 500 (twice as big and regenerates twice as quickly) would have a power cost of 120k power/second - almost 8 times the power usage for double the size and double the regen rate.
So in the end, we are dividing a ships total shield capacity by its surface area, and multiplying the power cost per point of shield regen by the ships surface area.
While this setup may seem unnecessarily harsh on large ships, keep in mind that large ships still have an advantage over smaller ones in terms of how much armor they can have. I mentioned an idea concerning armor in the aforementioned thread where armor would be A) significantly buffed, and B) would deflect damage that would penetrate the armor, passing a percentage of it to the surrounding blocks instead. This thread originally discussed changes to cannons and beams to allow for base damage armor penetration regardless of subsystems. Under this new weapons system, if a block is destroyed half of the remaining damage goes to the block on the side directly opposite of the side impacted, while the rest is divided evenly amongst the other 4 surrounding blocks. With this idea, destroyed armor blocks would still protect the blocks behind them by decreasing the penetrating damage while increasing the radial damage to the blocks sharing that surface - and since these would most likely also be armor blocks, the combined effect would be a shot that would destroy 1 armor block and weaken the others, but would not significantly damage the soft blocks behind the armor block.
Of course, while armor would last longer and be more effective, it would still degrade as it got hit and unlike shields would not regenerate. Since the armor can't be repaired/replaced easily during combat, it would be more effective on larger ships with more of it.
So basically, what I am suggesting with both of these ideas is to increase the protective effect of armor, while at the same time making shields more power-intensive and less effective as ship size increases. Larger ships would need to rely more on their armor for protection when surviving a firefight, whereas smaller ships with less armor would have shields to protect them instead. This would change the dynamic of gameplay significantly, as well as keep people from building these massive bleeding titans with 9-figure shield capacities that can tank indefinitely.
Of course, this only fixes the defensive aspect - offensively larger ships will still have an advantage over smaller ones in terms of raw damage output. But a smaller ship is faster, lighter, and harder to hit, and without shields to protect it a group of small fighters could easily whittle down the armor and blocks of a larger ship, while the larger ship struggled to swat the flies taking bites out of it until it finally keeled over and died, metaphorically speaking. It would also make it to where even missile-pulse combos with massive alpha damage would not be able to 1-shot an unshielded ship... through it may be able to using a 1-2 punch, one to blow a hole in the armor and one to blow up what is inside. But of course, smart shipwrights could mitigate that risk by using armor internally as well and compartmentalizing the different areas of their ship.