The main risk in using a piece of software like Game Maker is that it may influence how you develop your game. You might have a really creative idea, but if Game Maker lacks an existing template for implementing that idea, will you still attempt it?
Building a game from the ground up is considerably harder, but offers a much greater incentive to build the engine to meet your exact needs.
The decision ultimately comes down to two questions; how unique will your game be? are you going to let the design of GM restrict or influence that uniqueness?