The dialogue in the single issues was very different than that in the collection. In the Joker's collected edition, much of the titular character's mocking flirtation was censored, or at the very least, toned down. The editorial changes can be seen in an album here.
Suicide Squad was forced to tie into the storyline due to Harley being in the book. Needless to say (as stated in the Writer Revolt entry) Adam Glass does his damnedest to downplay the forced tie-in screwing up his storyline.
Gail Simone was fired off the book very suddenly by an incoming editor via e-mail, resulting in the fall-out of Batgirl's contribution to the storyline being given to a fill-in writer. After a massive fan-support by the internet, Gail was not only rehired back on as the on-going writer, but managed to, more or less, go in the direction she had wanted.
What Could Have Been: Several writers had requested editorial to use Cassandra Cain and Stephanie Brown in their stories.
Adam Glass really didn't like having to tie into the storyline; after the forced tie-ins, he starts issue #16 off right when the last pre-Death In the Family issue leaves off and doesn't bring it up again. Glass also used his tie-ins to expand on Snyder's first two issues of the storyline, revealing that Harley was blackmailed into helping the Joker and have her and Joker fight it out as far as Harley rejecting the Joker and trying to bring him to justice.
J.H. Williams and Grant Morrison outright refused to have their storylines derailed by the crossover and as such, Batwoman and Batman Incorporated both are not part of it.