Firstly, getting the AI to use the right equipment, and present a more varied challenge (well tougher at higher ranks), should be a lot higher on the list - to the point where I was *personally* very disappointed that the AI changes Sarah mentioned for 1.4 seemed to disappear. Surely if players are going to create 'pvp' ships, stacked to the gunwales with PCBs, then, for a level playing field it would be nice for the AI to have the same option. Likewise, no AI should be flying around without any form of shields.
Secondly, the 'Devil's Advocate' argument you make for commanders not sticking around is, I feel, a good argument for SCB removal - it encourages more cowardly, life-preserving and 'realistic' gameplay. I'd rather more commanders (and AI) ran from combat, than sticking around to be annihilated, just so the player can rack up kill counts to combat Elite, and...
Thirdly, without limiting SCBs to one per ship, or having another mechanic to limit their use, we get into a situation where the large ships, such as the Python and Anaconda, are consistently used in a combat role, which I would argue is against their original presentation in the previous games a pure trading ships, reliant on turrets for defence (albeit with the possibility for large, fixed mounted weapons that you wouldn't want to get in front of. There is also too much of a gap between ship capabilities already - a pack of Eagles or Sidewinders should be a serious threat to an Anaconda, no matter how expensive or well-equipped the bigger ship. Small ships should not necessarily just be 'annoying road-bumps' for bigger ones.
Following on from the above, however, the idea of 'overcharging' shields, with excess energy going into heat build-up/module damage if not dissipated seems a good one (if we ignore what form of energy shields are converting incoming projectiles and beams into anyway?

).
Oh, and AI wingmen - to protect those SCB-less, large trade ships? When?