Basically, this was a design decision from a gameplay perspective. Making focused fire too effective would make people who micromanage battles way too powerful. So instead of big fleets firing weapons all over the place and having cool battles, players would be forced to micro manage every battle instead of relying on the excellent Fleet system they have in.
My suggest is that while shield mitigation is a decent enough system and explanation for this gameplay mechanic, I'm thinking you could tone it down bit then add (or just add) another system that comes from a tabletop miniature wargame about fleet scale starship combat.
The idea is basically Suppression Fire, much like infantry ground combat. It sounds a bit silly, but it's not a bad rational. Basically, as starships take hits and the weapons explode on their shields or hull, the ship shakes, crews get rattled, finely tuned weapons get thrown slightly off target before being readjusted. Shield flares and explosions blind sensors, defense grids have to be prioritized and adjusted, and classic scifi stuff happens like control panels explode on the bridge.
The gameplay effect of this would be that ships under fire, even if it doesn't immediately kill the ships, still makes them less effective, giving a player an incentive to make sure all enemy ships are under fire.
