The system would have to remember how many wanted ships got destroyed
It already does - the daily bounty report includes the number of claimed bounties.
Missions are already submitted one at a time.
Disaggregating exploration data so it didn't matter if you turned in a page or one at a time should be easy (and Frontier presumably have an interest in *not* encouraging people to repeatedly generate small transactions)
Trade has already been mostly disaggregated and that could be continued (though I think rewarding mixed-commodity loads up to a point is a good thing)
It's just bounties and bonds where
- you don't have an option to split them up
- the optimal behaviour is so counter-intuitively different to the behaviour the game hints at it feels like a bug.
I don't buy the "black box" arguments on that one - absolutely, the BGS should remain undocumented in its specifics and reward research and thought. But you could apply the same argument to the rule:
"handing in combat bonds during a war reduces that side's influence".
Black box, very easily discoverable by research, not particularly intuitive so rewards experts ... also would I think be considered a bug by 99%+ of players if it ever got implemented.
Certainly it's possible to sit in an engineered ship/wing in a RES or CZ and invincibly rack up bounties indefinitely. But that's a problem to be solved in the NPC encounter design - CZs especially need a redesign anyway to have more interesting scenarios than "brawl in random bit of empty space" - not in the BGS. In the transactional model it's even easier to do because pretty much any ship is capable of dropping into a CZ, splashing an Eagle or Taipan, and jumping out. With a bit of luck with CZ locations and careful use of nav locks, you could even skip most of the delays on flight time.
Automatic disaggregation of bounties (so still transactional, but a bounty is a bounty whether it was for an Eagle or an Anaconda) should be practical.