I'd probably build the Bat as a heavily cybered infiltration specialist, probably with some expensive bioware. Skip out on IP boosters; you're striking from darkness and dont need it. Instead, take Reaction and Agility boosts, and any 'ware that helps soak damage. Maybe an Attention Coprocessor.
I'd also recommed 1500 karma karmagen, or 600bp
Qualities get tricky. Bruce Wayne could really have a ton of positive and negative qualities. Definitely some Phobias (friendships), Compulsions (to fight crime, never kill, never use firearms, really Bruce's head is all screwed up). Flashbacks are also a definite, as possibly Big Regret, SINner, Wanted, Distinctive Style, Records on File, and possibly Vindictive.
On the other hand, I could see Genetic Optimization, Erased, Guts, toxin resistance, a lot of martial arts abilities, First Impression, and possibbly some things to simulate his wealth of contacts.