I'd like to propose several things :
Something similar to Ranger's Voley skills for an easier aiming. Without this, naphta barrels are completely useless. It cost a lot just to do few test shots to estimate its landing. With Trebuchet Trajectory, archers on a wall would be less safe. Defenders could shoot back and prepare some 'fire power' to counter large enemy numbers.
Yes, trajectory would be difficult implement due to different ammo types as stone ammo and barrel for comparison have different range. That is why suggesting:
Trebuchet ammo queue
In case there is more than 1 type of ammo (could be a cow, god knows what people are shooting these days), all ammo appear in an ammo queue. Operator could switch ammo within it and trajectory of a trebuchet would be determined by an ammo type that is first in queue.
Forced tunnel collapse
Long time ago, I brought this question before MMO started. Unfortunately it was discarded without much putting thought in it, because questions were filtered by AMA 'hosts'. I'll bring this matter once again. We do need a mechanic to force tunnel to callpse immediately. It ocurred a number times,when tunnels are used as a base defense and therefore impossible to set up trebuchet. My suggestion is to make use of sapper charges for this matter. When it explodes in a tunnel any kind or depth, it would force mine to collapse right away during JH. Strategic investment to siege somebody, but stops griefers simply destroy vast number of tunnels.
With those mechanics implemented I could see more than just round/square castles in MMO world, but also small anti-siege camps with trebuchets around main base. Trebuchets strategically established with ammo and under ground passages for retreat (last time checked, enemy cannot dig tunnels during JH in my land, maybe someone could confirm it) and as retreat happens sapper charge used to close connection between anti-siege tower and main base.