Batman Begins is better than most superhero movies - darker and more realistic - which is probably why so many people are bothering to explain what parts of the movie they found to be implausible, incoherent, or otherwise flawed.
[Mild Spoilers below, and Severe Spoilers at the other end of the link.]
A discussion at Agoraphilia includes comments on:
- the economics of intentionally causing a depression
- the economics of saving a city from a depression through philanthropy
- the coherence of the League of Shadows' efforts to save the city by destroying it
- the biochemistry of the fear-inducing toxin
- the feasibility of a microwave ray that vaporizes water without killing people directly
My view is that the movie manages to retain sufficient plausibility when dealing with the first three of these issues, while the last two fall under the "suspension of disbelief" exemption that is generally granted to technology in movies. My main concern, which you can read at Agoraphilia, is with strategic decisions by Batman and by the League of Shadows that seem designed to create drama rather than to achieve their goals.