Final Wars is a new continuity with connections to some of the Toho classics, much like Tokyo SOS. All of the kaiju have their original origins, or are pretty close to their original origins. Rodan and Angilas are still runamock mutants, Mothra is still the goddess of Infant Island, and King Seesar is presumably still the Azumi tribe's defender. Why he can't resist Xilian control as Mothra does is simple: that'd be another wrench thrown into the film's already crowded plot. I remember initial reports saying that Seesar was going to have a fight with Gigan. I was really looking forward to that. At least I'll be able to face them off in Unleashed!
By the way, I really dig Seesar's new design. In fact, I like it better than the original. Sure, it betrays the fact there's a human in there, but I really like the slim figure, the scales, and the neat, kept fur. Too bad we never got to see him use his reflective eyes.
"Vishnu takes on his multi-armed form, and says, "RAAAAAHHHOOO!!!'"