They could bought it for the setting, or they could buy it to finish off their potential rival (who also was sole king of the "samurai games") in order to not having to divide the pie of "people wanting to play samurai games" with AEG . If you can make a new setting and compete with already estabilished setting, OR kill that other setting and make your own, second decision is probably better; I mean, even during 2 years hiatus, people will probably go to your games because what else they have to do if they want to play card games? Go chase magic?
Gameplay comes first. Setting is secondary. If it was another way around, AEG wouldn't have to sell the game that was dying.