I've already made a blog post about what I'd like to see in Season 7 but it's looking very much like that won't happen (no great surprise; my idea was pretty much a fanfiction anyway).
Warning, this post may contain actual spoilers for season 7 of My Little Pony: Friendship is Magic!
What we do know about Season 7 already?
- From the IDW "Friendship is Magic" comics series (which have been written based on a season synposis and several episode scripts) that a mysterious pony called Shadowlock is erasing history books from libraries all over Equestria for some reason. Twilight defines them as 'the most important' books of history.
- We also know from more general marketing information is that the history of Equestria and of the Mane Six as individuals will be a running theme of Season 7.
My guess, is that Equestria's history and, specifically, how a certain continuum of events in history were key to the Mane Six becoming the ponies they are today, will be the central focus.
I'm pretty sure that Shadowlock is trying to erase knowledge of something from history using some kind of magic that interconnects written history with the actual knowledge held by some ponies. Although an antagonist, there will be some indication that he's acting out of desperation to erase some harm caused by knowledge of this part of history. Through 'things in our past' episodes for each of the Mane Six and the Princesses, we will see how this one set of events (like the Sonic Rainboom) connected them all together and shaped who they are today. As they are reminded of these important events (such as something involving Applejack's parents), it progressively breaks Shadowlock's spell until, eventually, they are all together able to recall the event the memory of which he was trying to suppress.
The finale will climax with the Mane Six having to decide whether to use the Rainbow Power to restore what was lost. It is at this point that the Mane Six will finally realise that Shadowlock isn't entirely a black hat and had a very good personal reason for wanting some things forgotten. What price knowing the truth when the truth has left innocent ponies (perhaps Shadowlock's family) harmed by the reputation history gives them? It's an extreme response on his part but I can see the Mane Six noting that the example of Starlight Glimmer showed that, in the face of personal loss or a sense of extreme injustice, some ponies react in extreme ways. I'm thinking that Twilight will able to find a happy medium rather than either a yes-or-no outcome but Shadowlock's spell will be broken.
A lovely epilogue scene would be for Celestia to trot over to Shadowlock and say to him: "In the end, all you ever had to do was ask me for justice and I would have granted it, My Little Pony."
He smiles sadly in response. "How could I believe that you would grant it if I couldn't believe that we were worthy of it myself, Princess?" At that point, Pinkie explodes onto shot in a shower of confetti and tells them to get back to the party.
Because I'm an Old Romantic
If my theory is right, I expect Princess Twilight Sparkle/Shadowlock shipping to become a thing. This is because Shadowlock will have the edgy anti-hero personality and behaviour needed for fans to cast him as Twilight's 'Dark Prince'.