Sure, cells keep your shields up, but in my experience, when I'm taking a lot of hits from a ship I can't hit very well, having more shields doesn't help me destroy them...
My first line of thought runs to some additional negative effect that triggers if a cell is used and the shield is not badly damaged, coupled with a longer delay between triggering a cell and receiving its benefits. In theory, this would mean that you would need to use a cell within a window of opportunity or risk A) leaving it too late and having the shield break or B) using it too soon and having something bad happen (like damage to your shield generator, or no benefit of the cell, etc.)
To your first point, I agree 100%. The module is completely defensive in Nature, but it does give MASSIVE surviveability, I'll admit to that.
To your second point, I know you said the plan is already to decrease ammunition (which I agree with) and to increase cost (the player in me groans because I use Cells a lot, the armchair game dev in me understands), but I'd just like to throw in my two cents on the "misuse" and "timing" mechanics being put more into play. E

, for me, focuses on the minute to minute gameplay, and it makes sense that hitting a Cell too early would overcharge and damage your shields. A slightly slower spool up time may add even more finess. Someone who's slamming down shields so fast that someone can't react won't have to worry about their shield cells, but use that cell too early, and you just handed them the advantage in the fight. If, say, overcharging your shield cell caused the over 100% to turn into heat energy (that energy has to go somewhere, right?) That's raw hull and module damage you just inflicted on yourself. Make it a high enough ratio (say, 25-30% heat damage for every X number of points over max shield health) and they may be hurting pretty bad.
I always find these nuanced solutions much more fun that just turning it into a gold sink. But, of course, I'm telling you nothing you haven't already heard/thought of. It's almost like you do this for a living or something... Weird...