Okay, here's what I got so far. Remember, this is based solely on Batman Begins, so please disregard the other media (comics, cartoons, batusi, etc...).
Stat-wise, he's not the stronger guy in the block (he's built, but he's not a Bane or Killer Croc). He is fast and knows how to make the best of his speed and ability to disappear. He can sure take a beating. He has a decent deductive mind and the ability to put 2 and 2 together (or a bat suit). He learns to have a preternatural knowledge of his surroundings. And he has a force of personality that allows him to make others think what he wants them to. This translates to Str 16(ish) Dex 18 Con 16 Int 14 Wis 17 Cha 18. What a munchkin!
As far as occupation goes, he clearly should have Dilettante. This puts his Wealth bonus up there, reflects his upper class upbrining, and gives him Intimidate as a class skill, no matter what classes he takes (important to get Frightful Presence later on). Since he's the main character, let's assume his Wealth is always at max (so he starts with at least +14 on his Wealth [+6 from occupation and max result on the 2d4]).
His first class looks like Dedicated. The movie Batman is smart, but not a genius. He learns to be fast and tough later in life. But it looks like he starts out as Dedicated. By the time he actually starts to train with the League of Shadows, he looks like Dedicated/Fast with some martial arts feats. His training as a ninja (or rather, NINJA!!!!) looks like an amalgam advanced class that mixes Martial Artist and Infiltrator.
As for feats, he must have all Martial Arts feats (combat, advanced, defensive...), the one that grants Frightful Presence,
That's all I got.