Joker is intelligent and has excellent foresight but Alfred the Butler, Michael Caine, provided the best understanding of Joker's motive, "He simply enjoys watching the world burn." Mixing his intelligence with a kick ass villain motive, dangerous motherfucker lol...
It was slightly disappointing to never find out where exactly the scars came from but i think they wanted to keep the Joker up on a pedestol so to speak. It is an obvious interest of anyone in Gotham on how he got those scars but never revealing keeps him from never being fully understood. The Joker was such a complex character and to figure out where his behavior was derived from could simplify or explain him to much.. for his comfort maybe..
I really do not think Two-Face is dead, especially with the Joker having to be written out of the 3rd one, it would be surprising to not carry over any of the villains..
I also didn't catch this until i thought about it after and maybe it was just slow of me but the Joker told Batman the wrong addresses for Rachel and Dent. I kind of shrugged it off in the movie and did not realize it...
And who saw the shit coming on the two boats? ill admit i thought the convicts were gonna blow up the other one, i really should have expected that..