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The idea of having "software slots" instead sounds interesting. But what would be the incentive for people to remove the training wheels for other things? I mean, what software could there be? I can only come up with those auto-pilot thingies and limpet controllers. Considering how limited use limpets see outside of mining and the fuel rats, i don't think that limpets would really replace the autopiloting software on many ships.
That being said, i also think that not adding new slots, but instead having 3 slots for software, which can be autopiloting software of limpet software, would still be an improvement. It would avoid the obvious power creep of the given upgrade, even if the incentive to replace the autopilot software would be very limited.