I would prefer a slower acceleration than lower speeds. Even with extra mass, you would need a more powerful engine system to accelerate a given vessel up to higher speeds. Which means higher energy expenditures. Simply saying 'heavy armor' is also an inadequate representation of the problem. The thicker the armor the heavier it becomes as well. Let us take Zesuaium for example (And hear me out) we have a vessel with .5 meters of Zesuaium plating, Zesuaium neither bends nor does it break. This means its innate mass and density are exceedingly high or have reached the point of infinite rigidity. It has even been documented canonically (It can be found if you dig somewhat deeper into the narrative) that it is a very heavy substance to the point that if it is used in a Daisy or Daisy II's shield it requires a sealed vacuum within to assist in this or require something akin to a NH-27, or Eihei to successfully lift and utilize. Even then I imagine the substance is not as thick as one would believe in regard to a Ketsurui Samurai's weapon but still lend enough weight to make it an effective tool. If we were to also apply the same reasoning to Nerimium, or Yamataium for example, Nerimum trumps Yamataium in overall mass due to its super dense nature.
While I can agree to a point, thickness of hull and material used within it, and such things as a framework should be taken into account as well. However, given the nature of propulsion technology reaching such incredibly high thrust to mass, this could possibly be counteracted to a degree thanks in part to the power sources these engines and propellants used. We're not talking about sitting on hundreds of tons of liquid oxygen propellant. But a form of exotic matter-based plasma in Turbo Aether. Particle Drives, CDD, and so on. I would also submit that the combined field systems could attribute to an overall reduction in the weight of a given vessel to help alleviate this problem. To what degree I neither know nor really care. Acceleration could and may likely be a more amenable consideration when propelling a ship with thick, heavy, and super-heavy armor materials. A Mindy does not have the sheer thickness of plate as a Plumeria, Azusa, Himiko or Sharie, or a Dreadnought. At best a Mindy with Zesuaium armor doesn't need thick plating due to its own combined field systems and the overall protective value Zesu provides as well as its natural manuverability as an effective combined defense. A micrometer of the substance from a purely narrative standpoint could tank multiple anti-personnel fires, up to anti-armor unless something truly nasty is used like Plasma, AM, or Aether itself. While it provides a protective value, the transferal of kinetic impact and the resulting energy may still be harmful to the pilot regardless.
While I may have gone off a self-important tangent and possibly failed in the explanation I'll try and put it in a more succinct fashion. Do I believe heavy armor should be penalized, yes? But in terms of acceleration, not top speed. This is splitting hairs on my part I know, I'm not wholly disagreeing with this idea. But trying to get my point across that mass should require more energy to accelerate and other consistencies of a given faction's technology are taken into account. The 'creep' will eventually arise regardless of whatever new system or proposal is put forth. Perhaps not for weeks, months or even a few years. But it can and will happen eventually. So any solutions we may come up with now may not work for tomorrow and the future's sake as people try to bypass this with 'more advanced' systems to wiggle around it despite rule enforcement or changes in how overall technology works in relation.