Have we considered the idea of adding a single dedicated size 1 "Computer" to the CORE slots that has the regular E through A Class options in terms of how many sub-functions it can perform laid out in Outfitting like the bays in an SRV hangar?
Along the lines of the hoppers in a refinery you could have say, a Class A with 6 programs while the D only has 3 but gets the typical mass benefits for exploration. It's a mandatory core item but doesn't scale like the life support or sensors on big ships.
ADC and Supercruise assist could come as standard, filling both function slots in the default Class E for the brand new player and if they want to try their hand at mining in the freewinder they can refit for prospector and collector limpet controllers instead.
The programs themselves could be supplied as some kind of physical punch card and stored / sorted / transferred via a separate panel in Outfitting as an adjunct to engineering with the best ones a 'treasure' to find, as mission rewards or upgrades.
Many, many games with legs include the concept of following clues and mission instructions to find chests, break them open and loot the treasure as seen in the current materials loops but what about when we can finally EVA into surface bases?
Prior to that, if legs are limited to inside the ship, going down to the "Babbage Bay" to physically swap out the subroutines and reprogram (I vote for "Daisy, Daisy" ambiance music) for say, an emergency fuel transfer or hull repair might be pretty awesome!
Of course, then we'd need a personal inventory, and sidearms, etc, etc...
Edit: Afterthought...
You could still have E through A Class limpet programs on the cards themselves, to emulate the current modules, with the best hatch breakers only available in high tech anarchy systems, where a PYR8 would expect to find them.
Maybe the more expensive civilian and military Supercruise Assist could include advanced interdiction resistance, or the ability to avoid the trade lanes completely and gain extra speed by staying off the ecliptic plane or using gravity wells?
Ooh, ooh! How about a set of cards that give a phasing sequence bonus, or a shield modulation calculator against shield tanks, or maybe an armour piercing, penetrating or high yield bonus that stacks with hull damage engineering?
Edit: Continued ramblings,
here...