The only real flaws in it I would say are mostly to do with the 3rd act, particularly the whole fear gas in Gotham and Arkam Asylum release. I just thought The Scarecrow should have been left alone once Ra's Al Ghul showed up, Scarecrow running around Gotham just causing mayhem in an already chaotic situation with just a horse and his fists is pretty stupid. And the way he just got tased off by Rachel and ran away whelping was pathetic...it almost ruined scarecrow, who up to that point was pretty cool and psychologically intimidating.
I love the Ra's Al Ghul reveal in Wayne Manor and Ra's big philosophical speech, that's probably the best part of the movie..but the rest of the 3rd act is kinda disappointing just because how great the first 2 acts were.
Only thing wrong with the first act was I feel that Ken Wanttanbee/the fake Ra's should have at least a little bit more screen time in the 1st act, he's supposed to be Ra's Al Ghul so I wish the audience would have been fooled by it more, be he basically only gets only 2 minutes of screen time speaking maybe like 3 sentences..mostly in Japanese.
Another complaint is the fight scenes are too shaky, it worked really good in the first time Batman appears on the docs but for the rest of the movie it's annoying, didnt really care much for the Monorail Batman-Ra's fight.. couldn't see much..camera too close up and too shaky.
I didn't think Katie Holmes was that bad, she looked a little too young even though she's 27 there she almost looks 18. But I'd rather look at her face than that bridge troll mug of Maggie Gyllenhaal and in The Dark Knight Rachel's character seems fickle.
But with these complaints aside, the movie still deserves a 9/10 IMO. It's far superior to the Batmans that came before it, yes including Tim Burtan's first Batman film. I still like it more than The Dark Knight, and The Dark Knight Rises although I realize i'll always be in a minority there. I think the Alfred-Bruce relationship is strongest in this film, I thought Liam Neeson's Ra's Al Ghul was an excellence mentor and I love his traditionalist good guy in the extreme type of villain aspect to him. I enjoy the scenes of the Young Bruce with his father. I think the over all design of Gotham in this film is more original than it was in the sequals, in TDK it seems exactly like Chicago, no beautiful monorail or slight Gothic scenes. And most importantly I like and identify with Bruce's journey and becoming. It's an origin story.
So yeah despite a few flaws i'd fix it's still a great movie.