First of all ... if you look at different airlines, you'll see that some charge for bicycles and some don't and the amount they charge varies. This site will give you an idea of that, but you'd have to look up the individual airlines for confirmation as they tend to change their charges and rules and regs frequently.
http://www.ibike.org/encouragement/travel/bagregs.htm
As for bringing everything else as carry-on, what many of us do is to put our empty panniers into the cardboard bicycle box for padding ... and then put the contents of the panniers into a lightweight duffle bag which can be folded up and stuffed into the bottom of a pannier once we get cycling.
This was how we arranged things on our most recent tour ... bicycle box with panniers as padding, larger woven blue bags with the camping gear, blue and green duffle bags with clothing, and we each had purple backpacks, but in this picture, Rowan is using his handlebar bag instead of the backpacks.
The duffle bags and backpacks folded down to a very small size ...
