I kinda skim through most of the stuff I read. Not sure it's because I've spent to much time on the computer, or if it's because of my Attention Deficit Disorder.
How did Queen Chrysalis capture the Mane Six (beyond shape-shifting)?
Who is Cozy Glow and why is she evil?
Where is the real Grogar?
Who are Spike's real parents?
Did Twilight know that the Tree of Harmony could talk to ponies and other creatures using a magical doppelganger of her?