In the past two years I have read about a half dozen sets of seige rules. I've read Christopher Duffy's "Fire and Stone". I've read the Osprey "Fortress" on Vauban fortification (rather derivative text, brilliant colour illustrations). I've even read the article in the 1983 Military Modelling annual on this same subject. Naturally I now consider myself to be an expert.
On the basis of this deep research a few points seem salient.
*There will be two time-scales operating - strategic and tactical. The tactical move might be declared at either the end of the strategic move and needs to be enacted on the table. The strategic move might be defined as "as long as it takes to do 'x'" - with 'x' being something like opening a parallel, or building a redoubt, or driving a sap forward or building a certain number of gabions.
*Per strategic move each player ought to be able to expend a certain number of "build points" to construct or repair works. This number ought to be based on the number of available troops. There ought never be quite enough of these "build points". Perhaps it might be better to call them engineering points. Some of your regiments will NEVER condescend to do manual labour - Maison du Roi anyone?
*On the strategic scale of things, a battery of seige guns ought to have a certain "batter" value equivalent to the number of guns. Per strategic move this ought to be subtracted from a target's build point total and modified further by the build points a defender is prepared to expend maintining the works.
*Parallels should be opened in one movement virtually by the whole army and ought to each take about a night to provide the necessary protection.
*Ricochet batteries. Their task is to demolish the traverses within the covered way. once their points value is reduced to zero, the covered way is untenable and troops in this sector must withdraw to the ravelin or bastion behind.
*Sapping forward. As you sap more closely to the fortress your trenches should become shorter and possibly more acutely angled - ie, progress should be slower as you progress. Perhaps they should cost more build points?
*Mining. Best not done without an umpire. Still, strategic move by strategic move attacker and defender could cut their mines and counter-mines with both sides making their listen rolls (sounds like CoC!) and the umpire ruling that the mine was detected. The map moves made by attacker and defender could be marked on the umpires master map. Intersecting tunnells would trigger a tactical move of underground combat. Mines would produce a zone of destruction relative to the charge placed therein. The amount of powder placed in the mine needs to be limited. Building tunnels costs build points per inch driven. A fortress ought to start the game with a number of listening galeries already built.
I see seiges as being campaigns in their own right. As such, the only real question is how complicated do you want to get? I think supply rules would have a place in determining the limits on the beseiger in terms of what resources they can bring to bear.
More as I think it up...