As a combatives-certified US Army soldier, I can say that body armor in an urban combative situation changes the parameters of self-defense measures.
Generally, most pistol calibers are sufficient (in the hands of the proficient and properly trained) for defending one's self against even armed aggressors. But when someone dons bullet proof or bullet resistant armors, engagement tactics must adapt accordingly.
I have no idea what type of body armor that monster in Colorado was wearing, but I am fully aware of the abilities and limitations of US Army body armor.
The body armor issued in the US Army will stop up to 10 5.56mm/.223 rounds (depending on angle), or 3-4 7.62mm rounds (depending on angle), up to 20 9mm rounds, and several .45 ACP rounds.
As for how to best engage someone wearing similar armor, it depends on your weapon of choice and level of skill. If you have a standard caliber handgun, your best bet is to dump as many rounds into center mass of the assailant as continually as possible in order to distract and possibly subdue him. Since accuracy is more difficult in a dark theatre setting with possible distances beyond 20 feet, you don't want to risk missing a head shot and increasing the risk of collateral damage to bystanders.
My personal advice is to use the assailant's body armor to your advantage. The armor required to stop multiple bullet impacts is often heavy and cumbersome, especially to someone not used to it, and even more so if the assailant is covered in the armor. Use that knowledge to try to tackle or overpower the assailant rather than try to pound your way through the armor with ammunition.
That said, if more Americans use their constitutional right to arm themselves, the guy could have been brought down by a barrage of self defensive projectiles from his intended victims instead of the tragic opposite.