You're way off with the general time here. When Jaina first came to Kalimdor she was in conflict with the horde (if you remember from warcraft 3). Her views changed after she and Thrall both came into contact with the "prophet" who told them they had to unite to stop the burning legion.
Theramore makes more sense over Kul'Tiras for these reasons:
-Theramore is in a position with more expansion oportunities (also they would probably end up fighting the horde over land as both factions try to expand)
-We have already thought up most of Theramore's unit roster
-Kul'Tiras would be too cramped, surrounded by Lordaeron and Khaz Modan.
-We have planned Kul'Tiras to be a city of Lordaeron at the start of the campaign
One thing I would like to stress is that this is Warcraft: Total War and not world of warcraft total war. This mod begins roughly around the begining of Warcraft 3, please try to remember that