Hi Volt_Cruelerz. You missed some things in my post.
by having three capital ships with separate damage types, you can almost completely negate mitigation as they fire in series, thus confusing the shield and destroying the concept
My original post: "(But don't let AI flip back and forth between almost similar mitigation potentials! That would cause a "thrashing", and the shields may never mitigate any hits at all. There should be a threshold, say "choose best mitigation type if it is X points more than current type".)"
you could have different bars that would show what damage type was dealing the most damage. Each would mitigate independently
My original post: "A ship being hit will have to decide which weapon class type to defeat. It's shield mitigation would only work for 1 weapon class type at any one time. (Please display which type the mitigation is currently targetting.)"
Simply put, don't mess with the system.. It would be such an overhaul that it would take sims up to V 10.999 You don't want such a drastic change...
I agree. But I would change the manual to explain this form of shield mitigation.
Think of mitigation as "kinetic capacitors" that store up damage energy (kinetic energy) from incoming weapons fire. The more the incoming kinetic energy (damage), the more charged up the kinetic capacitors will be, improving their efficacy.
Kinetic capacitors can work by spreading incoming energy to the surrounding space. Changing the vector of incoming energy will require energy itself. A low-charged kinetic capacitor can only deflect incoming energy to a small angle outwards, therefore still letting through significant damage. A high-charged kinetic capacitor has more energy/ability to deflect incoming damage to a larger angle outwards, thereby effecting a higher level of damage mitigation.
Also, this explanation will follow for how ships don't get holes punched in them enough to allow loss of crew. Secondary shields still hold the mitigation effect over the entire hull, after primary shields have been depleted. Secondary shields also make use of kinetic capacitors to spread damage over the hull, so a ship is either completely holding or entirely exploding. (Save for external systems leaking antimatter, of course).
Lastly, all capacitors in real life lose their charge over time, so shield mitigation decays over time.
Since you're writing a book, let me give some suggestions.

A loud bang announces the arrival of the fleet. The space behind them violently claps back together after being forcefully pried open for phase jump.
Captain Pike looks apprehensively across the wide image at the front of the bridge. Forward visuals are composed by multiple hidden cameras in the exterior hull. Space-faring ships today have no windows, no vulnerable openings for incoming weapons fire or sudden solar flares. All is serene, the nearby planet peacefully aglow in the warmth of the distant sun.
"Bam!". Another loud bang. The Kol shakes violently under a sudden impact.
The new tactical officer, Pavel Chekov, snaps to attention instantly. "Shields down! Secondary shields online. Kinetic capacitors charged up to max. Mitigation at 67%".
A miscalculated phase jump? A collision? Where's the enemy? Pike is at once confused and angry. Intelligence didn't say anything, as usual.
A painfully long 8 seconds passes, silent. Conn officer Niobe Watts is poised to take evasive action.
"Space anomaly to port side!", screams Pavel.
A large ship of alien design looks like it is shedding a cloak of transparent fabric. Advanced local phase technology, Pike thinks. Sneaky bastards.
"Evasive action, sir?", asks Niobe, loud and imploring. Fear grips the entire bridge instantly.
"No use running from an enemy ship after just 1 hit", Pike says in as calm and controlled a manner as he can. "There could be more enemies around. We don't want to be tricked into the arms of a larger beast".
Pike knows that the crew is safe, as long as the hull holds. Today's kinetic capacitor technology is able to spread damage over the entire hull, preventing debilitating punches that could poke holes in the hull and leech crew out to space.
A second blast shakes the ship violently. "Hull rating down to 80%!". Pavel scrambles over the controls to monitor and adjust defence systems. "4 more hits to bring us down, sir!".
The 2 Hoshikos behind are already moving up to send repair bots.
At almost the same time, 2 Domina Subjugators decloaked around the first enemy ship. What? The Advent has acquired new cloaking technology so soon?
"Fire all weapons on the subjators now", Pike says as calmly as before. Pike can feel the fear slipping away. The bridge knows its captain has made a good gamble.
"All weapons opening on subjators now, sir", Pavel responds. "Antimatter readings on the first ship is low."
"Good", Pike heaved a sigh of relief ever so slightly. "2 boulders in 10 seconds is enough for now."