The organisation of gamemaker's interface and workflow is cleaner and better than Construct, IMO. You have sprites, objects and rooms - draw a sprite, assign it to an object, give the object actions and events, put it in a room, and hey presto - a game! Every component of the game is available in an organised tree structure on the left hand side - sprites, objects, rooms, fonts, sounds, backgrounds, timelines, paths and scripts.
Obviously, Construct's workflow is hugely different, but I still think it could benefit from a central library panel like some other programs (e.g. Adobe Flash). Right now, all the different parts are spread out all over the place, and you can't access all functions from all parts and modes of the UI.
Also, another thing that I think Construct could benefit from is the inclusion of a proper tilemap system. The current method combining sprites and tiled backgrounds (as found in Deadeye's platform school) still feels like a hack or a workaround for something that is quite a fundamental feature of many 2D games and engines. I don't know how it would fit in the current workflow, but I think it's something that should be added in some form.