Here is my list of possible Season 6 episodes. This is all speculation as we know next to nothing about S6. So don't be surprised if none of these happen.
S06E01+2: Corruption of the Cutie: A new villain appears in this two parter written by Meghan McCarthy this time with the power to possess the bodies of ponies using their Cutie Marks and uses their powers to bring Equestria to ruin. They have since taken over Rainbow Dash. Can our heroines defeat this evil and save Rainbow before it's too late?
S06E03: Princess Moondancer: Ever since Moondancer moved to Ponyville, a rift has began appearing between Princess Twilight and her friends.
S06E04: All that Glimmers...: Starlight Glimmer has invited the people of Cutie Town to a feast at Princess Twilight's castle. But Starlight has never cooked before and everything she tries ends up making ponies cringe or get sick. It's up to Master Chef Pinkie Pie to save the banquet.
S06E05: Wingin' It: Rainbow Dash's first official preformance with the Wonderbolts is about to begin as an air show, but Rainbow forgot to invite her friends. Wracked with guilt, she sends them VIP passes out of her own wallet. Unfortunately, she got lost in the big city of Mareami and must get to her preformance before it starts.
S06E06: Air Farce: Rarity takes over Rainbow Dash's weather pony duties after losing a bet, and has to help the weather ponies once again raise the water to Cloudsdale. However, Rarity's bad experience with controlling the weather and difficulty gettimg the pegasi to respect her worries Rainbow Dash. What's more is a few ponies are out of shape. Can she, with the help of Scootaloo bring the weather ponies up to speed in time to bring the water up to Cloudsdale?
More coming soon. Tell me what you think in the comments.