1: Change ballista ammunition type to a non stackable item called "Rack of bolts" that isnt type:bolt. Additional change to its firing script would then allow you to load multiple "Rack of Bolts" into the ballistae in one go, and then each time you fire it, it uses up one of the "rack of bolt" items in it's inventory.
This saves opening PC inventory each time to "reload", gets rid of the "stack splitting" for bolt types from 99, and makes it so that ballista are pre set racks of bolts that slot into place in one go to fire it, not time consuming reloads.
2: Catapult aiming. Have a catapult aiming widget which allows you to target a certain ground area for the catapult. Upon firing it, the catapult aims at roughly that position, with a certain randomness and lands as close as the random effect determines.
If each catapult had a way of knowing who had the aiming widget, you could put the catapults in the gate courtyard, and have someone play "spotter" who targets the floor, and a "firer" who fires the catapult via the lever.
This may also allow further ranged targeting with catapults if the spotter scouts out ahead and marks a position. I spoken command could mark the spot, or an item use, depending. If it was spoken, scouts could do it in stealth.
3: keep ballista away from the edges of walls because the aiming pc needs to be close to it, but able to see over the edge of the wall
4: make it so ballistae cant shoot friendlies who are not infront of them. I've noticed they have a tendancy to shoot friendlies if it's "get next Thing" cycles onto a PC. Not sure how to adjust the targeting method to avoid this.
5: Add animation to catapult firing. I couldnt tell when i'd fired the catapult whether it Had fired, until I saw a flamestrike animation in the distance. Perhaps a sound burst expanding radial animation will do.
Thrawn Note: I apologise on editing this. Hit edit instead of quote, and ended up deleting part of the post. Not sure what kind of animation you are looking for. The catapult arm animation isn't bioware, and requires a hak.