Hey, another Discord regular here. I feel that we should define what a Meson Cannon, in the context of game balance is. A Meson Cannon is an option that allows you to ignore or at least diminish an enemies static defensive capabilities, in this case armor and shields, while dealing little damage beyond that effect. It needs to be less effective at long ranges then most other beam weapons. It is uniquely specialized at destroying large ships, no matter how much space is dedicated to defenses
A redesign of the Meson would, I think, begin in the first point. Instead of always ignoring the enemy, it should instead have conditions that need to be met for the effect to apply. The previous suggestion of armor of a certain thickness blocking it is good, but that takes away its role of killing heavily defended ships and instead shifts it to an anti-shield weapon (something which the Microwave already takes up, partially, although I think some reworking should be considered there too). Perhaps a system where "Radiation" or "McGuffin Juice" or whatever you want to call it builds up around a ship, decided entirely by its size and not shield/armor, which will allow mesons to then bypass these defenses freely once it exists in large enough quantities. Larger mesons would create more radiation but not deal more damage, as one seems more then enough. This would make the choice of Meson size an interesting choice, as the raw DPS of more cannons would be weighed against the amount of radiation needed for that DPS to be made a reality.
Alternatively you could have a percentage chance for penetration similar to hit chance that depends on range, otherwise it just hits the armor.
That's my two cents anyway