Olive Branch is planning something with trying to get everyone to turn against CelestiaI mean, it'd probably make sense if there was some end goal for him to achieve other than "make the ruler look bad".
Said plan has to do with DiscordHe's mentioned a few times throughout the story, and it could be considered foreshadowing... Also, Olive Branch is attempting to have a rebellion of sorts. And what do Rebellions usually cause? Chaos.
If this happens and Discord breaks free, he'll pull an Eviler than Thou on Olive and become the Big BadHe's also the last villain to have the Elements be used on, and one of Rainbow Dash's worries when she talked with Soarin' was that the Elements might have not worked, what with what happened before. It might be used to produce some final closure on that matter.
Alternatively, Olive Branch is doing this as a Roaring Rampage of Revenge against CelestiaSomething must have happened during the Changeling invasion that caused Olive to become jaded enough to attack Celestia. Perhaps he lost a loved one?
Pinkie and Scootaloo's storylines will intertwine.Specifically, when Speedy Delivery is outed as abusing Scoots, it will cause Clyde to have a Jerkass Realization in regards to how he treated Pinkie.
Olive Branch will be executed, as will Speedy Delivery and Quick Delivery.They are participating in a plan to overthrow the legal government of Equestria. If that's not high treason, I don't know what is. Now that they have assaulted and likely kidnapped a member of the extended royal family, it seems increasingly likely that they will end up on the gallows.
Alternatively, they'll be banished..."Well that's not so bad compared to-" "To the moon... or even the sun."
Alternatively he will get his wishBut it comes with some consequences…
During the meeting with Celestia, Olive Branch will try to let the fact that Twilight tried to warn them be revealedOne of his arguments he presented in the beginning of the arc was the unexplained absence of Twilight, and people would start to ask questions about why Twilight appeared with the real Cadance (like where did she come from, what was she doing, what caused her to be there in the first place), so it's natural that at some point, Celestia or Olive Branch will mention that fact and this will be the lynchpin that Olive wants so much. Sort of jossed. He already knew about that and used it as blackmail against Celestia.
Rainbow Dash wasn't really bored by the Daring Do fanzine; it was just Too Soon.
The conspirators are ChangelingsWhen Twilight tried to scan one of the ponies to see if they were a Changeling, she gained a splitting headache... This could probably indicate that they're Changelings. Either they are Chrysalis' men who are enacting phase two of an elaborate plan (stage one is the Wedding, including her failure) to seize control of Equestria or a separate hive who are using the situation to their advantage.
There's more to the plan than just kidnapping the Mane Six to use as hostagesIn all honesty, Celestia would probably roast Olive Branch upon noticing he has her student and her friends hostage so there's probably more to his plan than just "Step down from your position of Godly Princess who can smite us with a single whim or we will hurt your pets!"
Olive Branch will be defeated with an Engineered Public ConfessionSpecifically, the fact that he engineered Garble's gang's attack. I doubt he or his group will have much standing even among the Gullible Lemmings if that knowledge goes public.
Speedy Delivery and Olive Branch will end up dead by the end of the story.Wouldn't that be a satisfactory ending for those two wonderful ponies?
If the story continues after Families, it will proceed to deconstruct the Alternate Character Interpretations of the Mane SixFamilies deconstructed two popular fanfic ideas, Scootabuse and Tyrant Celestia and fitted them into the Post-Canterlot Wedding setting. Perhaps the continuing story may pick at Psycho Pinkie and Incest Twilight.
Discord as the Bigger Bad.It's evident the stories' theme is Forgiveness and Discord in the Nuptialverse will be defeated once and for all when he's been forgiven despite the atrocities he's committed. Because it hurts him and he gains his powers from everyone hating him. In the end, even he will go through a Villainous Breakdown why the others pity or feel remorse for him. With Twilight giving a Kirk Summation.
Magical Mystery Cure will happen at some point, but it'd end with Twilight calling out Celestia for the crap she put her friends throughOr someone else.
Chrysalis' partner in Direction.At the end of Families, Chrysalis is directed to another agent of Discord's, to work on a plan to free him, and the first chapter of Direction has them moving ahead on it, though without revealing who this other being is. Possibilities:
Direction will deconstruct Easily ForgivenWe have several characters who have been hit with this trope (Discord, Trixie, and Shimmer) and at least one of them has crossed so far into the Moral Event Horizon that forgiveness isn't an option.