another good reason for them to go back to johto is they can finally develop some of the characters like the odd gym leaders could make a cameo. also they might decide to have team rocket make a return as an evil group to return the show to its roots and where it all started. lets face it team rocket are always refered back to in the show thanks to jessie and james. so they could find some reason to have the whole team in the show again. also there are only 5 brains i believe in the sinnoh battle frontier so they would have to find a way to make it stretch out a bit. also if they did go back to johto and dawn did a load of new contests, it would be cool to see her up against drew, harley and soledad.
They had the opportunity to do that in Kanto, yet they totally blew it. And if they went to Johto theres no garante any of Mays rivals will be there. They most likely will have gotten 5 ribbons, competed in the grand festival and moved onto a new region by the time the Filler saga comes around.
It just makes more sense to go to the battle island. In Emerald, the battle frontier had no story or anything to connect it to the plot, and it wasn't big enough to accomodate an entire journey. The battle island in Sinnoh has loads more to offer, and is much bigger. It has links with the rest of the game through character and storyline and provides great opportunity for story continuation (Stark mountain and such), it also has the contest resort place, which they could stretch to include contests as well, giving Dawn a storyline.
Also, thee have been several hints of Ash taking on the Elite 4 this series. with there being only 5 battle frontier buildings, it might make sense to have Ash use the battle frontier to train up to battle the elite 4 at the end of the filler. Why on earth would Ash go all the way back to Johto, then go all the way back to Sinnoh for a few battles, only to have to come all the way back again.
And the reason everyone thinks the anime will follow the games is because the anime DOES follow the games as much as it possibly can. Or at least it has since Hoenn started. There wasnt enough in the Emerald battle frontier to fill another series with so the moved it to Kanto and made up some fillers. They have the opportunity to adapt from the game here, so why would they miss it?