This is straight from Yoshi-P's mouth. Does it not sound like he considers the SUE events to be different and separate from the original quest line? Does it not seem like he considers the original quest-line to NOT lead up to 2.0?
No. It sounds like he's saying exactly what I am. The SUE events are filling in the blanks. Once the Grand Compant aspect is established they'll bring all the main scenario stuff up to speed. It's still all just a prologue to 2.0.