To me, this points to a serious flaw in the base system.
I can understand how you might come to that conclusion. I disagree though.
The base game is the game at its simplest. That would be a space game where people can build ships. Everyone has the same tools and resources to work with thus the game is already balanced as much as it can ever be.
You can pretty much link most the issues in the game to the attempts to limit players or to create a balance where there shouldn't be or unnatural balance.
If for example fighters and light craft where actually given tools to perform the roles they are better suited at rather than trying to give them some sort of unnatural bonus then people would have more options and greater need to use small craft.
They overly relied on power as a limiter in so many instances, Small craft have a power boost while large ships have a cap. No ways close to reality. Most air craft carriers can out run most the rest of the fleet. Same if you look at space craft and designs for concept ones. While we may not have all the tech at hand to build some of them we can still calculate power and plan accordingly to determine what is needed. A good example of stuff calculated can be seen in this video
. Advancements our knowledge in warp theory have lead to designs that would require far smaller amounts of power needed to the point we have a potentially viable design idea floored.
Small craft usually make good scout, recon, surveillance, interceptors, precision targeting, you know hitting points that say a capital ship might not be directly able to target.
In this game you can't use fighters to get passed shields because in this game shields resembles more closely Star Trek Hull integrity field.
Cloaking they chose to limit via power, as they did weapons groups by power and so on. That is some what understandable from the position they where at in the start of development. They really didn't have much else to work with. Power was the one deciding thing you could restrict or control on pretty much everything.
However, they could have limited cloaking by several other means thus making small craft more suited for full use of cloaking and while allowing other craft to use it limiting their ability with it because of size.
That could easily been done by limiting the maximum cloaking effect while moving and using two points to measure to reduces its effect. Speed and mass of object. Instead of increasing power requirements they could have simply limited the alpha of the object.
In short the real issue is the mentality and clinking to the early practice from when the game was starting out. They don't need to any longer.
Instead of looking at limits via power and so on they should look for more realistic reasons things are could exist.
Take the issue with cloaking. They can have several legit reasons larger ships actually would be harder to cloak. Its a larger canvas to cover without distortions being visible. We know we can uses lenses today to actually reflect light around small objects. Its fairly simple with a small object but the larger it gets the harder it is not just cost wise for lenses but simply the distortion of trying to refract light in such around such a large area. I am sure you are familiar with a prism and how light is split into its wavelengths. Well the fact is that is an issue with all lenses. The larger it is the greater the issue is. So if you refract light around a large area those colored beams no longer line up as closely as they would have. In short the effect would be about like looking at a 3D movie without the glasses. You remember the Red Blue lens glasses.
Shields are another thing that do and don't make sense under the current system. Components handle X amount of power. You can limit the amount of power going to them in RL. Now you could say a shield that is charged requires very little power to maintain that charge. That would be do to stuff like capacitive leaking, power changes to heat.... and so on. Then under charging conditions it needs X amount of power to restore one point of a field energy. However there would be no difference at all under combat vs non-combat unless someone decided to push more power to shields. That would also result in much stronger shields if the rest of the system could handle increased power.
No military vessel in the world would employ a technology they couldn't control the power level to and it simply decide to use 10 times the power for no real reason. The US military (Navy) when it comes to stuff like this pretty much knows how much power everything is going to use and they account for it to the point where they know how much higher each day they need to pull the control rods to keep power up on their nuclear powered ships.
That said they could make use of weapons effects such as EMP to explain limited shield regeneration, power losses... You could even excuse it with something like it creates reverse power currents and so on. That is if you needed an explanation. Just saying doing stuff simply to limit something and doing it in the face of logic usually creates bad results.
Just think if light craft could rely on cloaking more then the reliance on shielding would be far less needed. Small craft aren't good for head to head confrontations. The modern day dog fight is measured in miles and seconds.
So in conclusion I see it as more a state of them needing to grow out of an old practice and not an issue with the base game.