Ok Clayface was the Joker, Talia, Strange and Ra are dead, the Joker dies and Clayface "dies". Also if you found the hints... Harley's pregnant.
These are just some things I noted about the ending:
Talia and Ra's bodies are missing when you go back to play the game after beating it. This should come as no suprise.... their followers will revive them.
During the boss fight, Clayface made multiple copies of himself.
Clayface falls into a lazarus pit... one surging with electricity..... No good could come from this.
Harley got pregnant while the Joker was still posioned by titan.
If you read the arkham city stories, the Joker actually gets trapped in AC after his escape from AI. When he dies, Batman carries his corpse outside AC.
So if they decide to bring the Joker back for a third game they have the following outs:
Ra's could revive him via a Lazarus pit seeing as how he's the only person ever to get the better of Batman.
Clayface mutates into some sort of Joker clone due to falling into the pit right after portraying the Joker.
The "real" Joker was yet another extension of Clayface.
Harley's baby, infected with titan, grows at a rapid pace, becoming essentially a new Joker. (Hey it's comic book logic.)
The Joker faked his death, and in doing so used Batman to break out of arkham city.
I honestly don't think they could make a third game without him and as well as it's selling, they will probably make a third game.
Thoughts?