Most people are predicting a Z legendary Pokemon but I'm also predicting a W legendary Pokemon like a few people. http://wiiuandmii.com/wp-content/uploads/2013/04/X-Y-logo-helix.png Pretty much everyone has pointed out that the Japanese X and Y logo has the double helix so the theme might be DNA which might have something to do with the new Mewtwo form.
Xerneas and Yveltal represent the X and Y sex determination system. http://en.wikipedia.org/wiki/XY_sex-determination_system
The Z and W Legendary Pokemon would represent the Z and W sex determination system http://en.wikipedia.org/wiki/ZW_sex-determination_system
The Z Legendary would be based on a Chinese Dragon and would be a Dragon/Fairy type Pokemon. A Chinese Dragon can easily form the letter Z like Xerneas forms X and Yveltal forms Y. It would be known as the "Fortune" Pokemon as the Chinese Dragon is known for being a symbol of good fortune and strength. http://cp.c-ij.com/en/contents/2022/03267/images/chinesedragon_thl.jpg
The W Legendary would be based on a giant Cuttlefish/Kraken like Pokemon. Why a cuttlefish? The Cuttlefish is known for having eyes that are shaped like the letter W and it's one of the few creatures or animals that can be used to form into a W with it's tentacles. http://upload.wikimedia.org/wikipedia/commons/c/cb/Georgia_Aquarium_-_Cuttlefish_Jan_2006.jpg I'm not quite sure what it would symbolize yet I've been thinking about it but it would be a Water/Poison type legendary Pokemon.
I'm bored so I kind of just started throwing things together.