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Here's what I do in RoA2: All AI nations have relations with each other set to -100 by default, and a pool of 'potential allies' are then picked with relations 50-100. By reducing the number of allies the AI can have, I reduce the chance of a cascading alliance and can address common problem areas (like greek states all allying each other).

I've been thinking about restricting this even further and making it so the AI is only permitted to ally each other by event, giving me complete control over who allies who so I can completely eliminate the problem.
 
Hmm, actually, I just realized that create_alliance is not in Rome, so much for that idea. For what I currently have, you're free to look at it and make use of it when I release RoA2 this weekend. I essentially just parse all AI countries at game start and adjust their relations with each other, then continually adjust relations over time via the maintenance events.