Hmm, yeah. I mean, it's definitely something I've been aware of, but haven't touched because of various concerns. For example, if the AI did this well, it might look "dumb" because it's not firing its weapons, especially if it made mistakes and also occasionally didn't fire when it should. There's also the risk of specific setups not firing certain weapons at all, if one isn't super careful about how to implement this.
That said, I think I have a better handle on how to go about this now, and making more loadouts player-AI-viable is a worthwhile goal. So: gave it a go, and I think I've got something that works pretty well.
The basic approach is it doesn't try to be perfect, but uses a sliding scale that includes its flux, enemy flux, and its soft flux, vs the shield-damage-factor, with a personality modifier thrown in for good measure. The sliding scale means there's a high tolerance to doing something inefficient initially but that drops quickly as the flux situation changes, meaning there's a low probability of certain weapons *never* getting fired, but it won't keep firing inefficient weapons for long.
For example, using the Heavy Blaster Medusa from the OP, it will fire the blasters once on approach (since soft flux is low, and so it's ok-ish to waste some flux, since it'll dissipate anyway - it's not optimal for sure, but I think it feels a lot better to do it regardless), but will then stop firing it and pretty much sticks to just railguns. The PL loadout will fire everything for a few seconds and then also fall back to railguns. This results in pretty much a tie between the two; if they weren't putting hard flux on shields with railguns, then they'd go back to using other weapons, at a rate that roughly matches the flux generation to dissipation.
Both loadouts also beat each other when the opponent is not using the new logic. Well, beat eventually - they consistently win the flux war in every engagement, but actually chasing down and finishing off a Medusa is another matter. What's nice is that it'll fire off HB shots after the enemy is forced to drop shields, so it's actually functioning in its intended role in the loadout.
The big thing, though, is that high-flux weapons should no longer cause many survivability problems, if at all.