I am most divided on this topic.
For one part I can understand and approve of the reasons the designers of TE present the Delphi Council the way they do. It's easier to provide new players and gamemasters with a starting platform. And just cause they are (or seem to be) the good guys at this point of the campaign doesn't mean this will stay the status quo later on, as Gargoyle pointed out previously.
Also, Quinn Sebastian being the way he currently is is a funny and admittedly easy way to explain some things.
On the other hand, as has also been pointed out previously, this is your
campaign. Make of it what you want. This wasn't different in oTorg and isn't different in other RPGs who use a metaplot. As a very ardent WoD
oWoD player and gamemaster I too have experiences with metaplots gone, err, wrong.
Use what you want, forget what you don't.
Infiniverse - as it had been and what I believe and hope will be again - represents the state of the official
game world. This isn't necessarily your game world. I even outright believe there had been no oTorg campaign that mirrored the Infiniverse newsletter one-hundred percent. The metaplot is a tool - nothing less and nothing more - to help you with fresh ideas (if you are in need of them) and to help you with the setting.
Also, please keep in mind that in oTorg at least the metaplot was in no small amount based on what the players decided or did. Did the majority of the groups foil Malraux's plan in adventure XYZ or did the villain succeed?