As Pokemon X and Y are almost there to be released, Pokemon Online will have to add all the new stuff those games are bringing with them. However, what is really bugging me about that regards 3D battles: altough PO won't probably have a 3D battle system as well, the problem with that regards all the new pokemons and Mega evolutions. In fact, all of them are 3D models now, with no sprites or whatsoever. So then, my question here is how the new Pokemons will be brought onto PO's battle windows? And about their moving animations? How will them be brought into PO decently without having to use such an enormous amount of time, maybe by using photogram per photogram tecniques? Those are my doubts, thanks for anyone that'll read this.
I can't speak for the developers, but all 3D models will be made up of individual frames, so it should be very easy to "sprite" all pokemon using the most appropriate frame of the animation, which will likely be fairly easy to obtain, assuming everything else in the games is.
Also you can turn on 2D on the 3DS, therefore won't you be able to produce a 2D image of them that could serve as a sprite?