I think a better way to deal with module inflation would be to restrict defensive modules to one per type, change the way the defensive modules work and adjust a lot of the engineering modifications and special effects.
Module reinforcement packages shouldn't exist at all. Instead there should be reinforced versions of core internals (other than B class).
Guardian Shield Boosters should add a percentage of the base ship shield value to the shields instead of a fixed boost.
Only 2 shield boosters installable at once.
Hull reinforcement should get removed and replaced by more bulkhead choices - some of the higher grade ones might even downgrade the size of all internal slots (it makes no sense that an internal component can affect the external armor of a ship).
Change the way small weapons work against larger ships (back to what it was before), turning them back into weapons from their current status of "special effect application devices that are otherwise completely useless".
Stop the limpet inflation - those things get programmed, the limpet controller should be able to program all types of limpets.
Adjust ship speed so that small ships are the fastest ships and not some of the larger medium sized ships. Same with agility - all small ships should be more agile than larger ships.
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In short: we need a complete rebalance