Yes, how the side missions in City started were pretty chaotic, but that didn't turn me off completely. There were a few times where I raged because it wasn't clear to me on how to progress
Especially the Deadshot side mission
Also, me not being a hardcore gamer, the New Game+ is friggin IMPOSSIBLE for me. The first group of random baddies, I couldn't beat on New Game+, which sucks because
I wanted to hear the second special ending with Harley singing to the baby
I'm normally pretty apathetic toward video game plots and storylines, but the twists in the story in City was fan-friggin-tasic.
How they handled the main plotline with Joker/Clayface
Thou I was a little disappointed that
Nightwing shows up, says a couple lines, then is never heard from again. Granted, I haven't downloaded the Nightwing DLC which might add a lot more.
There's alot of unfinished business with cliffhangers and such that would promise a sequel
Scarecrow's boat, Azazel talking about the Ashes of Arkham, the Hush bit, Black Mask breaking out. Ra's Al Ghul's body moving etc.
I'd be gutted if they didn't do one, I loved both games and their take on the batman universe.
Oh, but on the baby front:
In the Harlequin DLC you find the cot with many more pregnancy tests around it, all negative.