[Mephisto]

Real challenge only comes with real players. there are some ways to give the AI a better start. Start the game with a good planet, this will prevent the Ai from running out of resources early on (this often cripples the AI for the whole game). Don't play in maps with many black holes.
Many AIs relay on mines for defense. Not necessarily against a player but at least against other players. You can cripple some of the races by disallowing mines.
Same for PPBs: Many races relay on them. If you disallow them, they will stuck be stuck to DUC for quite a while.
The AI can use training facilities but only if the fleets aren't used elsewhere. However, disallowing the whole advanced tech tree will cripple the anti-cloak strategy of many races. just don't use training facilities but don't disallow this tech area.
Be very careful with what you disallow. Not using it is fine, disallowing it prevents many AI races from working as designed by their modders!