You can safely change most bosses' AI using the Ifrit enemy editor custom version JWP made a while back. Just be careful when editing enemies that appear alongside others, as this can lead to the known issues (broken graphics in battles, softlocks etc). In such cases, you can still make smaller changes to an enemy's AI by opening the respective c0m.dat files with a hex editor. For example, when searching for the byte sequence 02 02 03, you are often directly at the beginning of the AI section (this is the code that makes most enemies skip their turns with a probability of 33%), which is really helpful if you just want to change some numbers using the hex editor, without fundamentally changing the AI.
So all in all, I'm just using Ifrit and hex editor where necessary. I don't know of any other program that change enemy AI. But who knows, maybe Ifrit gets another update some time in the future.