One notable omission, relating to the necessity for multiple applications instead of one, is the inability of Illustrator to pass linked or embedded images to an external editor. The only Adobe-based workaround of which I’m aware is to use Acrobat’s “Object Touch-Up” tool to get the image from an AI-included PDF into Photoshop—assuming it’s not in indexed or spot colour, in which case it has to be converted first. Yet FreeHand (like InDesign and some other non-Adobe applications, QuarkXpress for example) has been able to do this trick for many years!
Another glaring weakness of AI’s I didn’t see mentioned is the lack of adjustable tab-stops, among other text-formatting deficiencies requiring Adobe-only users to compose even the simplest tabular layouts in ID instead, or to use multiple separate AI text-boxes with the consequent loss of editing convenience.