AI is mostly hard coded, so there isn't much that modders can do with it. Updates have to come from Creative Assembly.
What they have done at Rome: Total Realism is make it so the enemy uses more formations depending on the situation. While this doesn't really make them smarter, it makes it a little more challenging and a little less predictable. There are still many AI problems particularly, as you mentioned, in siege battles. But these can't be fixed by the mod team.
HOWEVER... Rome: Total Realism makes the game 10x better. I can't go back to the Vanilla version of the game. Just isn't any fun (and I thought it was awesome at first before trying R:TR). They have done so much to improve the game in so many different ways. I bought the expansion (Barbarian Invasion) but uninstalled it and went back to Rome: Total Realism because it just wasn't playable after playing the mod. They are currently working on RTR 7.0 which will be compatable with the new updates and the expansion, and then I will reinstall it. I would highly reccomend installing the Modification. It makes and already great game one of the best games of all time.
Make sure you go to
www.rometotalrealism.org
DO NOT GO TO the .com (rometotalrealism.com). This is a fake site and may contain malicious (sp?) code. What happened is one guy was stealing money from the team (donations to keep the site running). They found out and kicked him off. Unfortunatley, he owned the .com so they had to switch to .org.