Seeing as Filly Funtasia is a show whose trailers and as such all official video material currently number less than four minutes, theories are bound to run wild. Here's those that has seen some acknowledgement in some way.
"Cupcakes plot deduced"
After the October 2013 trailer became known, speculation on what was apparently scenes from one lone episode became a pastime, but almost all of it revolve around how Rose and possibly Bella made up a story about a monster to hide that they took the cupcakes themselves. Some small extra scenes in the April 2014 trailer provided water to the mill for those theories. The October 2013 trailer became known for placing its scenes completely out of order, but a pattern can be seen to some degree:
It begins with Will asking Rose where his cupcakes went. Rose comments the Bella didn't steal the cupcakes and that someone took it. Will is surprised by this, and so is Bella, at which point Rose looks sternly at Bella to pressure her. Bella and Lynn then decide to add wild details about who, or what, that stole them. When the teachers get word of the monster, they decide to go to extreme measures to get rid of the monster. Posters are put up in the hallways, and the students crowd around them, while Rose and Bella sneaks away and Rose points out that they have to tell the truth. As the two find a calm corner to talk in, Bella consider herself a hero, while Rose disagrees with this. The school Fillys prepare for a monster encounter, which Battiwigs notes to the Wizard of the Dark Mirror from a distance.
Will builds a complicated trap in the forest to catch the monster, but ends up catching Bella. After that there's a huge hole in information about how the problem is solved, apart from Battiwigs being smashed into a castle wall. Will prances happily with his discovered cupcakes, Rose gets a cupcake paper thrown in her face, and everyone laughs in the end.
There are some uncertainty as to which scenes are to be placed where, but this plot idea with some small variations form the basis for the discussion.
"There's a Filly world containing all brands"
Many of the sub-brands mention where their locations can be found. For instance, Papillia is in the south, the Filly Kingdom is across the sea from... something, Emocia is in the center of the "Filly kingdoms", and the Magical Land is within the Filly Kingdom. In addition, several official sources, most prominently a 2012 interview with the two founders of Dracco, refer to the Filly World as a setting with stories and locations of the Fillys.
Using Filly World for this does clash somewhat with the term Filly World also being used for a 2011 advent calendar with various Filly figures included.
"Gem transformation theory"
It revolves around that when Battiwigs and the Wizard of the Dark Mirror fell into a chest with a green gem and a red gem, they transformed into unusual kinds of Fillys, Al and Elio. Being as different from their usual selves as they are, they acquire Rose to assist them on a quest involving a blue gem that would turn them back to normal. As a result, Rose and Elio end up getting into Battiwigs and the Wizard's secret library base without Rose knowing what it is.
The two Fillys' lack of official names, and unusual appearances were considered supportive points for the theory, especially as angel and horn-wing Fillies were unheard of among the Filly Funtasia fandom. However, the theory was reduced to a curiosity after some months as the trailer's blue gem increased in its assumed importance, and Al became more considered as a travelling explorer and Elio as a general nerd.
"A Filly Angel or Pegasus brand is upcoming"
A set of Filly-like toys with pegasus wings were discovered on the Chinese toy-and-bootlegs site Taobao in June 2014, a site which were renowned among the My Little Pony fandom for showing off prototypes for upcoming official figures. This quickly turned speculation on a white Filly with pegasus wings from the April 2014 trailer into him being a show-off or ambassador for an upcoming Filly line.