Hm. Those are some very good points. Still... I wouldn't be too worried about beam kiting at the moment. To take Neonesis' Dominator versus HIL example, you need 2x HIL. Which means, at a minimum, 2x Sunder, or maybe 1x Odyssey - and, well, if I can't beat a single Dominator with that kind of force advantage, something is wrong, beam kiting or no beam kiting.
For me, at least, the damage boost from high flux just means that energy based ships get more dangerous as they take damage; it gives me an incentive to push the attack when my ship is getting high on flux, rather than playing safe and backing off to vent. And it just looks neat to have the guns glowing as you gain flux.
Also doesn't change the fact that the way the 'f' key works now is a pretty awkward way to go about it.
The fact that firing at nothing can accomplish the same thing isn't good, though.
This is really the biggest reason I can see for changing things. Hm. One possibly interesting thought: what if you increased energy weapon damage & flux generation by, say, 25% across the board - and then had high flux levels reduce flux cost of energy weapons instead of increasing damage? That would give some of the same feel of high flux = more firepower, keep the pretty glowing energy graphics for all ships, and totally remove any possible advantage to be had from artificially boosting your own flux levels.
I think that would combine fairly well with my HEF notion that naufrago linked to. But it'd need a fair bit of balance testing. On the other hand, just adding ship systems at all necessitates balance testing, so maybe now would be a good time to experiment?