Why does it have to be a timer? If there's a hard limit that is going to end the battle at some point, why use one that player has no influence over? Ammunition, for example, was one the player could influence - no more ammo means no more fight, but if you play smart and husband those rounds you can push that point back?
And really, why should the only reason that you can't thrash sector battle fleets with a string of frigates be "it takes too long"? Shouldn't the difficulty of what you're trying to accomplish just scale better?
Give each ship a zone of influence (larger than any weapon range so you can't just dance around outside it.) The bigger the ship, the bigger the zone; the better the ship's CR (or some other stat - maybe e-war or jamming, interdiction wells, whatever) the stronger the effect. Being within enemy zones increases your "suppression" value; supporting ships' friendly zones decrease it. If your suppression goes below the safe range, things start to get tough. Maybe:
- Weapon range and damage drops.
- Shield upkeep costs and damage ratios get worse.
- Maneuverability suffers.
- Beam warm-up time gets longer, teleport effects have a longer spin-up, weapon cooldowns get longer.
- Flux drains slower.
- Missiles lose flight time...
... and so on and so forth.
Fighting when massively outnumbered gets harder and harder on the ship until its performance goes so low that the player can't effectively keep up the kiting or evasion or whatever. You could still win a fight thus massively impaired, and the more glory to you if you can, but it's not just a counter with no other game effect. Don't make it hard to beat an entire fleet with a frigate because you just can't do it fast enough - make it hard to do because that fleet can drag you down and rip you apart.
Lore-wise it's electronic warfare (you don't even need "hacking" or anything so fancy - just massive jammers, aerosol clouds to break tight-beam comms, targeted saturation of detectors, electromagnetic effects setting up resonance effects in reactors, etc.) It's charged particulate clouds clogging up navigational deflectors, inductive heating effects overloading life support environmental controls, sparring radioactive decay inhibitors, clouds of dirt-cheap transponder beacons that make targeting computers work harder, whatever - the million and one tricks that ships have for making their enemies' lives harder and their own less so.