The inexplicability of the microwave weapon doesn't bother me in the slightest since it's a comic movie anyway...
But that's just it -- for the most part, it isn't a "comic movie." In most respects, it approaches the story with extreme realism, just about the most grounded take on a superhero film that's ever been done. So this element of pure, inane fantasy just seems out of place.
Besides, even a fantasy concept should be consistent within itself. The plan with the microwave generator doesn't make much internal sense. They develop a toxin that's only harmful if inhaled as a gas, then they spike the water supply with it and steal an experimental prototype device in order to vaporize the water? Who came up with that plan, Rube Goldberg? Why not just have the McGuffin be a device that sprays the gaseous toxin into the air directly? Or why not develop a form of the toxin that's effective in liquid form, so that spiking the water supply is sufficient by itself? The whole microwave-generator thing is stupid not only from a scientific standpoint, but from a logistical standpoint and a plot standpoint. It's an unnecessary and nonsensical complication. It only exists as a way for Wayne to be tipped off to an element of the bad guys' plan because the device was stolen from his own company, and there surely could've been a simpler way of getting to that point.