I don't necessarily disagree with the OP's idea but I'm not keen on just arbitrarily twiddling things to create the required "balance".
For me, the way to do it would be to start (and yes, I realise this is all a bit dull) by creating a spreadsheet of all the ships and then calculate each ship's attributes
CONSISTENTLY.
Once you've done that, you can look at all the ships, see which ones are out of whack and adjust their stat's in plausible ways (by giving them different modules and adjusting their internal slots etc) rather than just arbitrarily applying hidden "fiddle-factors" to various ships.
For example, consider the iCourier vs the iEagle.
The iCourier is significantly longer than an Eagle and
appears to have more "bulk".
The iCourier is, however,
lighter than the Eagle... and yet it has more integrity.
The iEagle uses the same thrusters as the iCourier and yet it is
faster than the iCourier despite being heavier.

If we (or, more importantly, FDev) had a spreadsheet that quantified each ship consistently then we might find that the iCourier has a surface area of, say, 100m² while the iEagle has a surface area of 75m².
If we start off assuming that the iCourier and iEagle have hulls built from the same material then the iEagle should be lighter than the iCourier.
If we
want the iCourier to be lighter than the iEagle then we have to reduce the thickness of the hull armor to do so... which would mean the iCourier's integrity is reduced as well.
If we adjust the iCourier's physical attributes and then find it's stupidly fast as a result, maybe we need to take away it's C3 thrusters and replace them with C2 thrusters.
Etc.
Point is, this would all be adjusted
consistently, using the physical attributes of the ship rather than just by applying hidden fiddle-factors which magically buff some ships and nerf others.
For me, that HAS to be the first step of any kind of ship re-balancing.
Any other tweaks to ships are simply castles built in sand.
The fundamental problem still remains.