Ponting said he thought Andrew Strauss would be chosen to lead the team to allow Flintoff to concentrate on his rehabilitation from an ankle injury.
''I did think Strauss would get the nod,'' Ponting told reporters in Kuala Lumpur after his team's 78-run win over the West Indies.
''They haven't gone that way, I don't know why, but we'll just have to wait and see what sort of job does when he arrives in Australia.'' Ponting said he was also surprised by England's decision to choose so many players under injury clouds.
Apart from all-rounder Flintoff, pace bowlers James Anderson (back) and Liam Plunkett (side) plus left-arm spinner Ashley Giles (hip) have fitness concerns.
England were badly beaten on their last Ashes tour to Australia when they arrived with several players fighting injuries and the upcoming series looms as a battle of the fittest with the five Tests crammed into seven weeks.
''They've got a few guys they'll be sweating on to see who comes up,'' Ponting said.
''But it doesn't really matter, it's irrelevant what they name, it doesn't change what we do.'' The Australian media also expressed its surprise at England's selection predicting the tourists would struggle.
''Tour after tour, England fails in Australia, partly because it asks too much of injured or under-prepared players,'' Brisbane's Courier Mail wrote.
''Each time it says it will learn. But four years later, the lesson has been forgotten.'' England won the Ashes in 2005 for the first time since 1987 with a 2-1 series victory on home soil. The first Test of the five-match Ashes series starts in Brisbane on November. 23.