Based on Snyder's comments about the upcoming "Dark Days: Metal" event, we're lead to believe many of the questions I (and other people) had about Snyder's run on "Batman" were actually Easter eggs he intentionally left for this event. I'm not entirely sure I buy that, but I'm also happy to have some of them answered, even if it's retroactively. One of the advantages of keeping a blog on comics is it helps you remember what you've read. Given my obsessive need to remember questions from previous stories, I went through my reviews of Snyder's 50-issue run and included the major questions here. I skipped some issue-specific questions (notably, the ones I had in issue #34), focusing mostly on the most obvious plot holes (and thus most likely to be retroactive Easter eggs). Notably, I couldn't force myself to re-read my reviews of "Batman Eternal" or (with less hesitation) "Batman and Robin Eternal." If Easter eggs are there, I'm just going to have to go without noticing them.
1) from "the Court of Owls" arc: How did the Court of Owls elude Bruce's notice for all that time? In "Death of the Family," Joker claims the Court of Owls gave Bruce so much trouble because he was distracted by the Bat-family. It's worth mentioning because Snyder is specifically acknowledging Bruce was off his game. But, he never gives us an alternate explanation, so, at this point, I guess we have to believe he agrees with Joker. Continuing on the theme, why did the Court emerge from the shadows for the Night of the Owls? How did it successfully return to said shadows (if it did)? Why did the Court turn against Lincoln March just as he was on the cusp of realizing the Court's investment in him by becoming Mayor? Most pressingly, how did it turn crippled Thomas Wayne, Jr. into strapping Lincoln March? (Dionesium definitely seems to play a role here, and I wouldn't be surprised if Owlman didn't appear in "Dark Days: Metal.") Why did the Court freeze former Talons, particularly since it didn't have the means of resurrecting them at the time? Did the Court know Bruce's identity?
2) from "the Death of the Family" arc: Why did Joker cut off his face? Did Joker know the Bat-families' identities? I don't want to rehash this argument too much, because it was already explored ad nauseum at the time. But, as a reminder, the tie-in issues in "Death of the Family" made it pretty clear Joker knew their identities (particularly the back-up story in "Red Hood and the Outlaws" #0). Joker kidnapped Barbara's mother, he destroyed Haly's circus, he knows what brand of soap Dick uses, he knew Jason's father was a deadbeat dad, etc. But, Bruce insisted Joker didn't know, because he once revealed his identity to him and Joker refused to acknowledge it. Snyder never has Bruce acknowledge the most plausible explanation for that: Joker might've conveniently forgot that information at the time but "remembered" it now. After all, at the start of the arc, Joker is shown as unhinged over the Bat-family dragging down Bruce. It makes sense he'd allow himself to "remember" their identities if he was so upset. (Issue #37 seems to confirm this point when Joker calls Batman "Bruce.") Conversely, does Bruce really know Joker's identity, as implied at the end of issue #17? Finally, what did Joker tell the members of the Bat-family when it came to what Bruce "really thought about them." This part was particularly ridiculous, since Sndyer established Joker didn't find some sort of super-secret dossier on the Bat-family he could share with them. But, in addition to the Bat-family's believing Joker did really know their identities, it's this information that helps drive the wedge between them and Bruce. As such, it's obviously relevant.
3) from the "Zero Year" arc: In issue #21, Riddler had some sort of card arrangement with phrases that I predicted would return one day as significant. Is that day now? In issue #23, Bruce opens a gem his father willed him that turns rooms seemingly into caves. It's so random, I have to assume it's one of the Easter eggs Snyder left on the way to "Dark Days." How did Riddler meet Dr. Death? Why was he using him to distract Batman? So he could plan Zero Year? In issue #29, Bruce tells Gordon he should've taken "the call" to avoid all the death that comes, but I wasn't sure what he meant; I didn't recall some call that could've avoided Riddler turning back the clock on Gotham or Dr. Death from doing whatever it was he was doing. Also, it was never clear to me how Riddler got access to the Red Hood Gang's files; it's an important point, because he uses them to build the army that patrols Gotham.
4) from issue #35: Bruce confronts the Justice League with a suit he built specifically for the occasion. During his conflict with the Flash, Capullo very carefully shows us a lightning bolt striking a Batarang. However, it doesn't have any impact on the battle; Batman wins by creating a frictionless surface to neutralize Barry. But, given the events of "The Button" cross-over event in "Batman" and "The Flash," it seems retroactively significant.
5) from the "Endgame" arc: We've never explicitly been told why Joker wanted to destroy the pool of dionesium under the Batcave. At the time, I hypothesized it was because he wanted to be the only one with access to dionesium (given the amount of it in his spine), but Snyder never spells out that part explicitly. Also, it's not entirely clear how Joker goes from battling Dick at the parade to arriving at the pool so quickly. In terms of the final conflict, I noted at the time Bruce seemed to have plenty of other options beyond dying and taking Joker with him. Snyder never really explained why he chose that route. Moreover, Alfred's explanation of the note Bruce left for him after he died -- reading only "HA!" -- didn't really make sense. He claims it was because Batman's story could've only ended in tragedy for people to believe in him (because he had to be mortal), but that doesn't seem to have anything to do with the word, "HA!"
6) from the "Superheavy" arc: Snyder never states how the dionesium that seeped through Bruce's cracked cranium changed the pathways in his brain. At the time, I just accepted it did. But, given the importance of dionesium to "Dark Days," it's probably worth noting here. Snyder also never explains how Peter Duggio survived the four gunshot wounds he received when the cop fired on him as he fled his burning bodega. At the time, I figured whatever Mr. Bloom gave him to grow wings retroactively healed the wounds, but Snyder never actually said that. After all, Peter went to his cousin Dylan before Dylan created Bloom, so I think we're supposed to believe Dylan also provided some sort of medical assistance. It's also never really clear how Duke gets clued into Bloom's existence. Gordon seems to learn of Bloom in issue #42 due to the Devil Pigs' connection to him, and Batman learns of him in issue #44 when he's investigating Peter's death. Duke knows enough about him to bring the seed Gordon gave Bruce to Dylan to investigate, but we don't know how he recognizes seed as coming from Bloom. Finally, almost everything about Geri Powers remains a mystery. For example, it seemed like Geri Powers might've given the thief who confronted Gordon in issue #41 the technology he used to do so, but we never get that confirmed. We also never learn why she was on her quest for an "island of stability" in the elements in the 200s. What was the point of creating Batmanium? Simply for science? I'm also not entirely sure why she and the Powers That Be never wanted Gordon looking into the Bloom case. After all, she never wound up having any connection to Bloom; in the end, he was just a homeless man who stole Dylan's seeds. Wouldn't she want Gordon stopping the villain destroying the city she now functionally controls? We're also not really sure what her plan was if Jim resigned as Batman as she wanted him to do, after he went rogue to investigate Bloom. Moving to other questions, Julia uses the Bat-signal to save Gordon because the Bat-signal apparently "holds" Rookie with an "electro-magnet" and such a magnet could counter Bloom's seeds, which are also "electro-magnetic." I never really understood why the robo suit was attached to the Bat-signal, but maybe Snyder had a reason. Finally, is it meaningful we learn Julie Madison is covered with tattoos, including an owl one?