I have started a new game with 1.06 and the 1.35 beta patch. So far, the AI is quite a challenge. Dramatically better than stock. Good thing I didn't give any AI bonus in game setup this time.
I have to agree that the designs with mixed missile/direct fire weapons are a mistake, as is using shields before they have reached the same level of effectiveness as armor.
Also, the AI needs to 'cleanup' more effectively after combat. My presence on a certain planet is disturbing a rival empire, and so it's under constant attack. After almost every battle, there is something 'left over' and sitting next to my planet. Supply ship, repair ship, etc. These should be sent home, not left sitting there like orphans. Sometimes I send some ships out to attack and destroy these logistics ships, but usually I'm too busy preparing for the next attack.