BEAMS! DEATH BY BEAMS! Okay, maybe not. Or death by bees.
One thing I'd like to see from a story POV is if you're forced to take a ship with two or three crewmembers (I.E. the Izra'il, the Uriel, the heavy bombers), that I'd like to see some interaction between the crew. Granted, Laporte's been flying mostly alone in her ship, but what are the odds she may get along with
the Weapon Systems Officer or Navigator in the back seat?
From a missions POV, I don't know if someone suggested this, but how about a mission like the second in Vassago's Dirge? Say, you have to take a Lapith and have to strike several minor capital targets across sections in high orbit of Earth and Mars, as in "jump, move fast, blow up targets or drop enough bombs so other strike packages can handle stragglers), jump out, re-load/repair, get to the next target, rinse and repeat," just to demonstrate how efficient precision strike bombing tactics can be. (Unless there was something in the lore description I overlooked regarding how fast the Lapith can recharge subspace drives without a burnout.)
Oh, and another cool thing I'd like to see: the Izra'il in action. Funnily enough after taking it out on a test fly, it feels like the F-15E Strike Eagle (maybe it's just me because of how the fighter looks and operates, or practically it's the only ship I can think of that can scarily do a lot of multi-role action like the GVB Sekhmet).