1. "Fixing" rules isn't easy!
Surprised by that?
It's easier just to criticize, but you took the hardest way...
2. Meson-screens-as-armour isn't working ... you need that "top penetrate" roll which knocks down the potency of the weapon, or the Meson hits come too readily.
When I suggested them to act as armor I never intended for the to penétrate rolls to be forfeited. Time ago I even suggested to reduce this armor factor by the roll over mínimum for penetration as a means to balance it, as I guess using both rules would make MG useless and unbalance it on the other side...
3. What is needed is some way to up the potency of the Particle Accelerator main armament, to give them a better chance of degrading the Meson attacks before they start registering significant numbers of hits. It may be that the way to do this is to scrap the rule that reduces the number of rolls a spinal PA gets by the target's armour factor - whilst leaving in place the full armour DM on the damage tables. This will mean that all a big-ass PA can do is fry the enemy's weapon systems ... but it will do it FAST.
One thing we sometimes forget is that PAs don't seem to be thought to be used against capital ships, but against auxiliaries and minor ships (as hamsters are). With their better to hit numbers and no effective screens against them, they are more likely to damage them (and a single weapon hit usually mission kills them, as their missiles become easier to stop).
4. There is still a need to balance down the amount of damage the Meson weaponry does when it scores a hit - and in particular, to prevent it from killing the entire crew many times over with almost every hit. Perhaps the way to do THIS is to limit the number of hits you can score on any system (including crew) to one hit per turn. Any surplus hits are lost; although if you roll several hits on the same system, you can always choose to have the most severe applied. This ruling will also help to ensure that those BIG ships truly can stand in line longer.
Remember the crew rules as crew sections instead of crew digits. That alone makes the crew hits quite less lethal, and more so as the ship is bigger.
5. I think the "oversize weapons always score at least one critical" ruling is worth persevering with as it does help to redress the balance in favour of the Particle Accelerators a bit.
should be testes, but I see interesting though in any case...