Due to the Spellstorm, I predict all cities with a large population of wizards will sustain severe damage and/or castrophic cultural change. This destruction will be brought about by the insanity of the wizards.
Cities afflicted by this will include, but not be limited to, Luskan, Waterdeep, the capital of Evermeet, the capital of Nimbral, Candlekeep, the capitals of Amn and Tethyr, all cities in Dambrath and Halruaa, all cities in Thay, all cities in Mulhorand, the capital of Aglarond, all cities in Cormyr, Shade Enclave, all cities on the Moonsea, most cities in Zahkara, many cities in Kara-Tur, and in most Underdark Cities. In Realmspace, all Spelljamming Ports will be afflicted, as magic is the basis for their existence.
Curiously, the illithid will not be affected at all, since they are psionic, not magical.
I think that, if the Alternative Reality of Abeir is merged with Toril, then Maztica will reunite with Faerun, geography and climate will change greatly, and Faerun will once more be the One Land.
I think peripherial areas will be especially subject to castrophic change. The Frozenfar may completely melt, Zakhara may alter it's position on the globe and it's shape and size, Evermeet may disappear or expand, the Hordelands will drastically alter (if Imaskari returns, or Damara, the Tuigan culture there will simply be overwhelmed.) The Raurin Desert, in my opinion, is one area that will undergo truly extreme change. Northern and equatorial Kara-Tur will probably alter beyond recognition. Maztica was never well defined, but may become so now.
The population of Toril is about to decrease in a major way. The Spellstorm will produce widespread anarchy, which will lead to something equivalent to World War. Crops will not be grown (or growable, perhaps), cities will be abandoned, trade collapse, and millions of people will starve. War and plague will decimate the survivors. The Black Death and ensuing One Hundred Years War in Europe are a good correlation (England dropped from 7 million to 2 million people.)
Most of the high level and mid level NPCs of Toril will perish, go insane, or change (if you have a PC wizard on Toril, it's high time to get out of town, as it were. Of course, your PC does not know what is coming, and by the time he or she does, it will be too late to flee, so ... better hope he or she makes that saving throw against insanity, and then find a nice deep hole to hide in for the next couple of decades.)