Love the mod. As far as im concerned, it has taken nilla civ's place. Thus thats why im posting this here rather than somewhere else. This mod IS civ from now on =)
Realistically (yes I know its pointless trying to back up a concept for a fantasy mod with realism, but stick with me here) When armies went to besiege a fortified location (city, fortress, etc) those armies built their seige weapons on site. Siege weapons were not built in a city somewhere (until the advent of cannon, which required established metalworking facilities). Catapults, onagers, trebuchets, siege towers, sap points, ladders and many others were constructed at the site of the siege.
While this concept might also work as a fully independent mod for regular civ, I think FfH's awesome promotions system would make it work flawlessly.
Certain units can be given Siege Engineer promotions to allow them to 'build' a siege weapon (like how fireballs are 'summoned'). Said siege weapons can do their dirty business. This might actually make the siege weapon suicide attack system bearable. Furthermore, war machines of various types might be constructed, such as ballista, scorpions and such as anti infantry weapons.
There it is. Review and amend at leisure.