Being able to manually increase flux levels isn't worthless, but... if the fight is going to be close, I always found it better to come in at zero flux and let enemy weapon fire build up my flux levels. And if I expected incoming damage to be low enough that I could afford to manually boost flux levels, well, that meant the enemy was toast anyway and it didn't matter.
That said, I've come up with a notion that would, for a few ships, make manual flux boosting actually a worthwhile tactical option;
see suggestion here.
Which you can do anyway by just firing off a few of your energy weapons before you are in range.
Besides, my trouble with energy weapons is trying to dissipate flux, not generate it.
Not necessarily; I much prefer to have flux dissipation at least equal to maximum flux generation. It's not always possible, especially if you're using heavy blasters - but, for an example, my standard Apogee design can fire its plasma cannon indefinitely without cumulative flux build-up.