I think it would be cool if siege engines could be connected to pressure plates, levers, and any other triggers that might be implemented. I suppose I just like the idea of a misstep by a goblin bringing death to the entire squad...Or maybe I don't like siege operators running off or something.
In any case, I think that ballistae, and possibly catapults, should be able to be connected to triggers. Obviously, ammo would have to be loaded by hand, so no Pull the Lever/R spams, but after that it can sit in the siege engine for years, if needed, until the lever is pulled. A siege engine would be pointed as normal, hooked up to a trigger, and loaded; after hooking the engine up, maybe it couldn't be fired by hand anymore. When the "trigger" signal was sent (i.e. the signal that opens doors and closes bridges), the siege engine would fire if it has ammo; when the "untrigger" signal was sent (i.e. the signal that closes doors and squashes stuff under bridges), nothing happens.
The siege engines would fire their projectile in a straight line, with a random, slight "tilt" off-center. Ballista arrows would do what they do now, catapult stones would...
I've probably left something out, but I think that that's it. As always, I welcome all thoughts and constructive criticism and scorn all non-constructive criticism.