9. Disrupted Ongoing Storylines
One of the reasons behind that anxiety laid in the fact that the company-wide relaunch would interfere with long-running arcs in the established canon. One such run that fell victim to this was, unfortunately, Grant Morrison's Batman, which was then engrossed in the final act of its five-year series.
Batman: Incorporated was designed to close Morrison's critically acclaimed stint on Batman, with a story that analysed the character's symbolism and what it actually meant to be the Dark Knight. It took the character out of the shadows in a move that saw Bruce Wayne publicly back the vigilante in his efforts to franchise the persona across the globe - a move that was typified by a return to the yellow and black crescent symbol on the character's newest Batsuit.
The whole mantra with that series was about Batman's ability to weaponise a public face as much as he is able to utilise the shadows, and yet the New 52 forced subsequent issues to eschew that design, despite the series existing in this weird, quasi-continuity between the old and new universe.
A slight redesign ended up erasing one of the series' coolest visual cues, and while Morrison managed to end his run on his own terms, it further added to the confusion regarding the new universe. While Morrison was writing Inc. - a story that only really made sense in the old continuity - Scott Snyder and Greg Capullo were doing their own thing with the Dark Knight, on a series that made no reference to Inc. or anything of the sort.
The reset just seemed to negate the importance of Morrison's run, and further exacerbated the wiggildy-piggildy state of the DCU as it then existed.