Maybe it's because they don't want to risk him and I don't think England as a team have entirely warmed to the 20/20 format as much as other countries.So why risk your premier bowler for riches much less appreciated then the bringing home of the ashes. Flintoff never seemed as passionate in the shorter format as the Test cricket. He seems to thrive as being the go to man, and 20/20 doesn't seem to suit him.
I feel the aussies would much rather face a Bresnan, who to be frank is never going to set the world on fire in the next 12 months, than a patilly fit Flintoff. Plus with Anderson, Swann and Broad in the side the only bowler who they maybe able to take advantage of is Onions if he plays, in 05 England had a few "freebie bowlers" in Gillespie, Tait and Kasperwicz.