im betting the 3rd version will go like this:
Isshu/Unova is experiencing black outs all over the region. The climate is getting colder, entire towns/areas begin to get flash frozen. The lack of heat is causing pokemon to go into hibernation (or some other predictable twist caused by the climate change/power outages). Team Plasma is trying to steal everyones pokemon,& gain control of Isshu/Unova while using Kyurem at their tool of destruction,making it freeze areas of Isshu/Unova (god thats annoying -_-"). You can catch all 3 dragons in this version (pretty much a staple in the series now). Kyurem gets its own cool (no pun intended) version of Mold Breaker, & its sginature attack Frozen World gets a power boost, along with a new attack it can learn at level 100 (imma dub it "Flash Freeze").
On a side note I'd like to see these changes:
We get more storyline,more back story on important characters, & the pokedex will be extended to include some more pokemon,& we can get the Fire/Bug egg sooner since IMO waiting til after E4 was pretty stupid& lame, it takes forever to evolve anyways, why does it matter if you got a lil caterpillar that shoots flames in your PC,or Team til you reach the E4,considering unless you grind it like hell from lv1, it wont be evolved by then :P