Aside from the inevitable "Death Star Trench Run" jokes, I've always wanted to undock from a big starship in my type f shuttle, fly inside a borg cube, and blow it up from the inside, all the while getting cover fire from a few other people who are flying their own fighters or runabouts.
An original gameplay style with its own unique rules could emerge from such STFs (Colliding with a ship, object or wall does damage to you, Defense scales with engine power, you can shoot while flying at full impulse, etc.)
It would also make sense from a business perspective since right now, the only reason you should buy an expensive peregrine fighter or delta flyer is for that one Vault mission that you could do with a free, slightly weaker type 8 shuttle.
Of course, all of this might be impossible due to (insert random TNG/DS9/VOY canon reference here) or "no man you see the game would be silly and stuff with shuttles everywhere...and stuff. hahaha lol my triplasma super magnetoplasma torpedo would deal 999999 damage to you haha lulz."
Shuttles and fighters need an overhaul for this to really work out. I refuse to buy the delta flyer and any fighters when i have the captains yact/charriot. there simply is no reason to get any of them from the Cstore. Well maybe the delta flyer but the KDF are pretty screwed in that area. The weapons in game need to be unslottable on small craft and a whole new line of shuttle only weapons need to be introduced. Its often we see auxillery craft holding its own against a full sized ships bearly getting hit constantly attacking subsystems like weapons and engions.
So i think shuttles should get target subsytems and fighters get a reinforce abillity to call in from 2-4 extra fighters. Also up the weapon slots on shuttles to 4 2-2 or 3-1 while fighters get 1 and the ability to equip special mines that drom 1 like bombs. The inate powers need there cooldown reduced to its rank 9 BOff comparison or simply increased to grade 3.
For Shuttle weapons ideas like,
Kenetic Bomb(mine replacer for fighters), drops a mine in the flavor of damige type EX Photon bomb these weapons have a lesser cooldown rate than normal mine luanchers, the single mine does not suffer from reduced damige like all shuttle weapons do.
Fighter cannons have lowered cool down rate and refire rate and when under the effects of rapid fire they look like and unbroken cain of cannon fire.
Heavy shuttle torpedoes are simply the same as regular torpedoes but with a slightly highercool down and are slottable on shuttles only.
Micro torpedoes are auxillery craft torpedoes luanchers and are slottable on all auxillery craft.