In the majority you’re quite right. A lot of comic writers don’t see the layers they just see the crazy fun clown. Which is unfortunate. A victim of bad writing as any comic character has suffered at one time or another. Too many fingers in the bread.
Batman is rather simple in my opinion, he’s obsessive compulsive to an extreme and given direction by anger and revenge. What are complex are his personal skills and methods, he’s pretty straight forward in the motivation department.
In that regard Joker and Bats have the compulsion thing in common but with a different target. The only thing Joker gives a damn about is Batman, everything he does is ‘for’ or about him.
The actors portrayal of him border on brilliance in my opinion but vary on motivations.
Mark Hamil had a very interesting perspective on him. An under appreciated genius trying to impress the only person that matters to him. Which is tragic because Batman would never really ‘get the joke’ so to speak. His flaw is this obsession but is dehumanized by mystery making him less a man and more a chaotic force which is why some of the better villains leave less explained because understanding of them makes them less imposing, but it depends on the type of villain you’re aiming for.
Villains are commonly seen as read between the lines type characters. Ledger’s Joker was fixated on one particular goal. Batman trying to rid Gotham of crime staying within rules (a form of control) doesn’t work, the only way to change things is chaos. He was proving a point to Batman, that’s all that matters to the Joker, ever in any story line, getting ‘his’ point across.
Just because the reason’s aren’t apparent doesn’t mean their aren’t any. Think of a magic trick, its awesome until you figure out how its done, then its kinda… "meh I could do that."
Joker is Flawed because his goal can never be achieved, like I said earlier Batman will never ‘get the joke’ and due to Bruce’s own twisted big brain he never will get it, Bats is a control-freak on a scary level so the concept of chaos being a benefit will never sit right.