Just some assorted comments, without necessarily addressing everything:
1) I've been thinking about a hullmod that turns shields over to AI control. Not as thrilled about adding an extra button to toggle this (or for ship lock-on), I think there are enough controls as it is. Might change my mind on it, but that's how I see it now.
2) Which ships, specifically, are you having trouble with? Part of this is ship design; ships that mainly rely on hardpoint weaponry should not, generally, have omni shields. This is the reason the Wolf and the Lasher got frontal shields in the last update, by the way.
As far as managing to pilot an omni-shield ship with hardpoints effectively, I think it's important to keep in mind that flux, not time-on-target is usually the limiting factor. So, stopping to fire to turn/handle your shields for a few seconds doesn't necessarily mean lost damage. It might mean a lost opportunity to fire at a vulnerable target, but that's a choice you make.
Putting bursty weapons in hardpoints is another way to make it work more smoothly. Finally, turn inertia is fairly accurate, so it's possible to keep on target for a short duration. I mean, you're not going to shoot down a Talon flying by, but if you're in a Medusa trying to keep a needler burst on an Eagle's shields, that's definitely doable.
Omni shields are pretty much strictly better than frontal, aren't they? I mean, they behave as frontal if you use turn-to-cursor and engage a single target, and they offer more flexibility that, admittedly, can be tricky to use well. And, yes, some of that is for "UI conflict" reasons, but still, that's all bonus compared to a frontal shield. Or am I missing something?