I think the main thing we'll take away from Killian in IM3 is that AIM is set up to be a recurring and powerful and sinister evil force that will have a presence in the MCU for years to come. The MCU version of SPECTRE, if you will. Killian will be an evil genius who's typically undone by his own ego, but he'll be shown to be just the tip of the iceberg when it comes to AIM. There'll be more evil geniuses and Scientist Supremes to take his place.
Yeah, I'm down with that. Set up AIM to be an organization that will continue to pose problems for SHIELD and our heroes throughout Cap2 and Ant-Man and possibly the SHIELD show.