May I suggest an idea?
How about
elite ships?
As in, they're not common, but when they're there, you'll KNOW it.
As in specific named ships that strike terror into the hearts of enemies on either side. Veteran ships with veteran captains and veteran crews of countless battles. Especially in regards to GTVA ships that have had Shivan fighting experience.
"You think think you frighten us? You're just humans, we've face far worse and won!"
They'd be very rare on the battlefield, but holy crap, when they show up, start panicking!
It would be especially cool if there were different grews that grew to be worth rivals and such. Specific named pilots on both sides that don't just die like flies like normal pilots. Ones that jump out automatically when their health hits a certain percentage.
It'll be nice too...
When the Shivans return and the two sides have to unite... I hope.

For example, when the GTVA Generation in Transcend rams through that Aeolus cruiser and just, doesn't, stop, coming after you mission after mission. I was honestly a little freaked out. How they hell am I gonna beat a guy obsessed with killing me in a po dunk fighter wing that's barely hanging on.