A Y class SYD-MEL will set you back close to $700 one way.Surely you are better off booking a standard flexi and paying the fare difference where applicable?

Not a fan of agents smit?I'll agree, not all of us are perfect, and people will make a mistake from time to time.May I ask how you book your travel?If you are as good at booking travel as your comment suggests, how about a round the world challenge? Oh wait, Expedia can't do that! 

Worst case scenario, you can look at the extra stop in either ORD and IAH.

If you are on separate tickets, then your luggage allowance would be based on each of the airlines separate policies.In this instance, I would pack light as I dought Aegean would be kind enough to give you the same allowance as Emirates.

When are you flying? Looking in GDS there are plenty of flights with business class.The connections through SCL however, are not pretty if this is what is important.