Changes to the The After Years include separating Ceodore's tale from Kain's, which was how it was in the original mobile phone release.
Ceodore's and Kain's original Challenge Dungeons are no longer merged.
Thus the developers wanted to create new content and create something to connect Final Fantasy IV with something that would happen right after the original game.
Final Fantasy IV: The Complete Collection uses 2D graphics rather than 3D like in the Nintendo DS version.
It features a chapter bridging the gap between the two stories called Final Fantasy IV -Interlude-.