Cyclops was killed so the actor could go work on a side-role in Superman Returns, at least that's what I heard...
And the Joker's back story isn't perfectly clear cut, but if you're talking about the fact that he's wearing makeup and isn't scarred by the vat of acid, or whatever, then, yeah, they didn't keep true to his story. Hell, they changed the way Two-Face was created too, but I think they did it realistically...so it wasn't bad in my book.