Their weakness is that they're not gods? They've evolved, physically or technologically, to the point of omnipotence. They've seen and built and done it all. But they can't do more than that. Their weakness is a lack of creativity beyond being creative enough to do everything? ...Does that make a lick of sense or is it verbal sophistry?
We shouldn't underestimate their abilities though. Their day at work could creating an entire multiverse and toying with every being and particle in it. Whatever their weaknesses, they must be to us as we are to bacteria or atoms or something.