Agreed about the distinction, but I think that the dev was talking about all three (bug fixes for 1, control updates for 2, unbalanced thruster pairs for 3 and a quote confirming that the current momentum delta between small and bigger ships is a balance measure).
I can personally see two problems with this approach. CIG has done well to implement a pretty extensive and complicated physics based simulation of the different thrusters that ships have. In essence, the goal here is to vary ship behavior according to the physical characteristics that they have, thus having things like battle damage, loadout, mass, cargo and different module quality directly affect the end behavior. This is pretty cool, since it also gives you the opportunity to dynamically change the behavior without having to prescribe different arbitrary states to the flight model for each hull.
The first problem stems from the fact that the ships we are testing now were made before the FM was locked, so its not easy to accommodate those mechanics. This brings out quirks like thruster placement and needed acceleration/output, center of mass/overall mass balance problems, the inability of non fixed thrusters to work as advertised due to acceleration lag, etc etc.
This has forced CIG to do two things at the same time. Hack and slash the IFCS and ship properties so that the hulls can fly properly, and try to re-design the ships so that they are compatible with the physics based model. So now we have ships with thrusters that are visualized in one place and actually fire from another in the hull, same level thrusters (quality, type and size) having completely different outputs from one hull to the other (and even from one side of the ship to the other), somewhat arbitrary mass numbers put in so as to make a ship behave properly, gimbaled thrusters working as fixed, ships having more thrusters in the flight model than what we see (viewable via asset hacking in the client and xml files), etc etc. Essentially, CIG has made a terrific flight model, only to fudge it so that the ships the artists made (and were sold to the playerbase before AC came out) do not feel like a drunk prostitute from Procyon trying to walk straight in a firestorm, and do not look like six big thrusters bolted into a sphere.
The second problem imo has to do with the direction CIG is taking regarding single seat fighter combat. This is a compound problem, since some of the factors that make the overall combat experience can be found again in the physics based model CIG has made. For example, the only way to make ships fly in coupled mode and feel nimble is to assign very powerful maneuvering thrusters to the hulls, thus making the ships have very fast accelerations in all directions. This removes problems with inertia and input lag from the system, but also makes the single seat ships behave like fast FPS turrets in space, with throttle management and maneuvering tactics playing second fiddle to aiming mechanics. If you add the very low TTK, the way gimbaled mounts work, and the fact that the FM forces the player to control 10 different axes directly (6dof for flying, 2 for aiming part of his ordnance, 2 for looking around) while not achieving controller balance (parity is impossible) the end result feels and looks like an arcade game. At least to me, that is.