I've noticed a general set of AI quirks while playing as a lone ship in campaign mode and setting myself to autopilot. The problems are mainly obvious with the paragon, but seem to be present with many other ships.
I find that often, not just sometimes, my autopiloted ship, despite having max flux dissipation, enormous flux capacity, 40 levels of character progression that include perks like 20% hard flux dissipation with shield raised and huge extra boosts to flux capacity and dissipation, and shield damage multipliers exceeding 0.35%, will randomly lower its shields or vent flux at the most inexplicable, inopportune moments, even while at very low (and getting lower already!) flux, yet while still well in range of enemy weapons, and even while surrounded and under fire, yet not enough fire to pose a threat if the shields had just remained up.
Distance from the enemy doesn't seem to matter. I can be on like 2000 out of 40,000 flux, or even at 0 flux, and my autopiloted ship will randomly drop shields or vent right in front of an enemy or group of enemies. A lot of these times it seems like my ship will drop shields after destroying an enemy, even at very low flux, and even if still surrounded or even flanked by more enemies. To a lesser degree of idiocy, the AI also likes to drop shields if close to topped out on soft flux, but at very little hard flux, while under fire or well within range of enemy weapons, rather than just keeping its shields up and waiting a little longer, and more safely, for the flux to drop while shielded, even if the damage being done to it is insignificant, opening itself up to needless armor and hull damage, and provoking alpha strikes of opportunity from missiles normally held in reserve.
This critically stupid, suicidal behavior seems above and beyond other quirks that make human control obviously superior, like the autopilot's tendency to sometimes charge into weapons range and attack an enemy that's at little or no flux, while the autopilot itself is nearly maxed on hard flux, when it has plenty of a speed and maneuverability advantage to back off, vent or dissipate, and then re-engage. While silly, at least it isn't pointlessly suicidal.
Observing the autopilot controlling a customized paragon also has me wondering if the AI doesn't at all understand that the ship it's controlling has a mod that gives it a front shield rather than an omni-shield, as a lot of the random shield drops seem to conveniently leave its flank exposed right as the shield re-engages. This could be coincidence, though.
I find that it's an absolute prerequisite to add accelerated shields as well on any front-shield modded ships that were previously using omni-shields, just to mitigate their tendencies to needlessly expose themselves.
[EDIT]:
I'm also suspicious that the AI doesn't realize its ship has the perk that gives the engine boost even at up to 25% flux, which may contribute to it dropping its shields to try to move faster.