I agree that is a problem. Bruce shouldn't be presented like that (from a comics faithfulness standpoint). He also shouldn't be given his entire arsenal by Lucius Fox, given all his best ideas by Ra's Al Ghul, etc. From a Batman mythos standpoint, I agree with you completely. From the standpoint of the movie itself and its themes, it works quite beautifully and enjoyably.
My thought on it is - every version of the Batman mythos has a different take on the character, some I agree with more than others. For example, I don't like Joker killing Bruce's parents in Batman '89 from a mythos standpoint, but I love how it works thematically in the story. I don't like the changes made in TDKR, and I think the way they work in the story are badly written and executed (I'm talking John Blake, Bruce retiring, etc.). In the case of Begins, its not the way I would have personally portrayed Bruce's motivation to leave Gotham but in the story itself it works well and quite beautifully, so I'm willing to run with it. I love the Thomas Wayne / Ra's Al Ghul antithesis in particular and think its quite compelling.
So I agree with you, but also kinda disagree.