A series bible is something of a first draft of the show, and ideas always evolve as time goes on. In this case, there are some things it would've been nice to see more of -- like Montoya partnering with Batman more than once*, more development for Summer Gleeson, and Riddler riddles that were actually intelligent and sophisticated (the riddles in his first two episodes were abysmal). And it's too bad that network censorship required them to tone down some of their ideas (the manhunt against Batman in "On Leather Wings" would've made more sense if he'd been suspected of killing as in the story outline rather than just stealing stuff and putting a guard in the hospital). But too many of the villain origins had a certain sameness to them -- Batman was somehow responsible for their deformation/madness and so they were on vendettas against him. I'm glad they went a different direction with Two-Face, having his vendetta be against Thorne, and especially I'm glad that Paul Dini gave us "Heart of Ice" instead of that cookie-cutter version of Mr. Freeze. I'm also glad Bruce ended up being written more sympathetically.
It's interesting to see the original Timm designs for Penguin and Catwoman before they were ordered to change them to be closer to the movie designs. Both would've been considerably better than what we got. They were finally able to restore the classic Penguin look for TNBA, but alas, we never got to see that cute long-haired Catwoman.
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*In fact, they kind of did something like this with Ellen Yin on The Batman.