Could you add some of that fancy battle formation stuff to this mod? It might make artillery too effective though.
Also, I believe that the engineering skill could use some love. Basically, have the actual availibility of siege engine construction be based on the party's engineering skill and have neutral engineers or other units operate them. Basically, if you have 1 engineering skill you can make simple constructions like earthworks for the battlefield. Make one construction type for every level of engineering and add a menu that allows you to choose which constructions to make.
Alternately, you can have a system of points relative to how many points of engineering skill you have available overall in your party. That is, allow the creation of certain engineering projects on-the-fly based on a total of expenditure of available engineering resources. So if the player had 10 engineering skill and 15 engineers with 1 point of engineering each, they would have a pool of 25 engineering resources. The player could then choose how to allocate these points before a battle. Each siege engine or defense option would have a relative resource and monetary cost. Earthworks (mounds of dirt used as walls) would have low point costs and probably no monetary cost while trebuchets and others would have higher point costs and significant price investments. Since it's rather unrealistic to allow an army to carry around a siege engine, simply make the engine a cash investment. When the battle is over, the player gets a return of gold based on the percentage of damage each siege engine sustained in combat (assuming that siege engines can take damage and be destroyed)
Have the construction work like this for AI lords as well. To do so, just add some engineering skill to enemy lords. Then when you go into battle you can be on the look-out for certain lords. I can see people saying, "Oh crap! It's Lord Rafarch and his ridiculously well-built siege engines." The AI will select which weapons and defense measures to use based on their party's combined engineering level and current gold. You could even make the palette of defense measures dependent on the culture. For example, Rhodoks would spend their engineering points on defensive measures like palisades and earthworks or ballistae to augment their elite spearmen and crossbow users.
Other ideas:
Sapping
With some scene-editing, add a tunnel under every available fortress and have it blocked by some removable terrain boulder/wall on both sides. With enough engineering points spent you can organize a raid under a wall instead of over it. Of course, once you're inside you might regret your choice.
Pungees
Spikes that can damage (or at least interrupt) horses that run into them.
Earthworks
Simple mounds of dirt with a steep front slope and a easy rear one to slow down cavalry or infantry.
Multiple ladders
More scene-editing. Allow the expenditure of extra engineering points to make more ramps available for attacking.
Levels of siege tower
More engineering resources and denars makes better siege towers with greater defenses. Skimp on the cost of engineers and you'll regret it as your soldiers are left weak and vulnerable.