I wouldn't mind if the Cloud flashback concerning the real story about him and Zack was a shortened version of Last Order with the Zack/Sephy fight.

Cissenei also never offended me, I would be cool with adding her in just to have a competent female Turk in the game, as long as she wasn't used to reference Before Crisis or Crisis Core in any way into the plot.

Other than that, none of it. I actually hope the ending is done in such a way to retcon Advent Children out of continuity by having Cloud perform a heroic sacrifice to stop Sephy or something, or go with the whole "humanity was wiped out" theory some fans have about the ending.