Kohlenstoff: Autofire should absolutely be set as part of automatic weapon assignment, excepting only missiles and strike-type weapons. Because here's the thing about an auto-assign: it's meant to be a low-effort useful configuration, something that is maybe not optimal, but also won't immediately shoot you in the foot. For an AI controlled ship, which groups are set to auto-fire by default is irrelevant; the AI will turn groups on and off as it thinks is appropriate. For the player, by contrast - well, you can -also- turn groups on or off if you need to during battle; your style of micro-managing which groups are active means you'll be doing a lot of that anyway, so whether it starts on or not shouldn't matter to you. By contrast, someone who doesn't tend to micro-manage their ship's guns (perhaps they built a variant that has enough flux vents to fire everything all the time) may take some time and confusion before they figure out why some of the guns they installed aren't shooting at things.
Overall, I have to agree with Atreg's suggestions; they're well thought out and would be an improvement to the game.