I agree siege weapons are a tremendous weapon in the AI arsenal, but simple military tactics can mitigate AI using them to great effect. Case in point. Ragnar was friends with no one but the Celts, but they were across the continent from me. Everyone surrounding me was friendly or pleased and hated Ragnar and Brennus. Eventually war broke out and I was asked to join in. Having no room for expansion, I knew this would be my opportunity to expand, and not upset any of my neighbors, so I sent a potent stack of artillery, calvary, and infantry.
It was 10 turns away to even reach the borders of Ragnar so I knew it wouldn't be easy to resupply. I was a little too cocky because Ragnar had cavalry, muskets, and grenadiers as his best units. I thought my artillery and infantry would kick butt, but as soon as I crossed his border I was hit by a stack with 4 trebs and assorted units that nearly took me down. I survived, but just barely. I lost only one unit, but all were badly damaged. I immediately sent all the reinforcements I could muster and began cranking units instead of buildings (I had been going for a cultural win). With my suviving stack I healed for a couple turns and headed for his nearest city. Luckily it was not heavily defended and I took the city which gave me a place to heal quicker. I holed up for a few turns and by the time I was ready to venture out, my reinforcements began to arrive. I moved on and took three more cities and then smacked his capital, and took it, but my stack was heavily damaged again, and I sat in the capital waiting to heal up again.
Here is the tactic that saved me. I set a cavalry unit out as a picket line to warn me of any approaching units from the direction I expected his forces to come. Sure enough here he came with 12 trebs and a rifleman. The condition of my units would have been devastated if he had gotten closer with the trebs. The cavalry unit attacked and retreated into the city and then every unit I had from the city attacked and even with diminshed strength, knocked the trebs down until there were only two left. The next turn I took them out and resupplied and healed. By the time I healed another stack of 10 trebs approached but my cavalry screen again warned me and I took them all out before they could bombard me. By that time I figured Ragnar must be on his last legs because the next stack that came was one catapult. I had to go to bed at that point, and will finish him off tonight, but it really taught me the importance of seeing what is coming and hitting the siege weapon stacks before they hit you.
Just some thoughts.