The teams I would select for Headingley, assuming all players fit:
Why? The pitch will be flat and swing has been far more effective in the series, hence Sidebottom in for Broad, and not Harmison. Bopara has not played remotely like a Test batsman in this series, so perhaps Trott should get his chance. Yes the batting looks a shade thinner, but Prior averages 46, Swann 35, and Anderson's batting has improved enough to easily be a number 9. Add to this the fact that the Australian bowling has not been good enough to bowl England out twice yet in the series and it's clear that the greater firepower is needed in England's bowling department. You have to back your top six to succeed and score the bulk of your runs. Additionally if the conditions look better suited to pace than spin I would be severely tempted to also play Harmison instead of Swann, as it is a good time to unleash him, and Headingley is not kind to spinners.
If however, Flintoff is not fit enough, and I don't think he should be playing at 50%:
Yes, I would select Harmison in place of Flintoff if he is not fit as England do need one proper hit-the-deck bowler (not a pea-shooter like Broad) for variety and there is none who does this better than Harmison. They will then need to retain either Broad or Swann for balance to the side, as both are in form with the bat and having one of them at 7 would be less of a gamble than playing both the debutant Trott and out-of-his-depth Bopara.
Sidebottom absolutely must play for several reasons - he is in form, he knows Headingley well, bowled amazingly in his previous Test here last year for match figures of 8/86, and crucially the Australians have never yet faced him, and do not play swing well, including left arm swing, as rookie Wayne Parnell showed earlier in the year. The selectors will want both Broad and Swann to play for their batting, but neither is likely to take bags of wickets at Headingley, so only one should play. I would like to see England's best 4 bowlers for the conditions (Anderson, Onions, Harmison, Sidebottom) play regardless of the batting, though this of course will never happen because they won't want to be perceived to have a long tail, although I would trust Anderson to hold the fort at number 8 based on his recent batting.
As for Australia, their ideal team at the moment would probably be:
Yes, Hughes not Watson, because Hughes is an exceptionally good opener who can make big hundreds, whereas Watson is a bit of a vain impostor who filled in for a couple of scratchy fifties on a flat deck. Watson has also shown he cannot be taken seriously as an allrounder. Hughes has only struggled against one bowler - Flintoff, and with Flintoff unlikely to bowl many overs at full pace or even play, Hughes should be backed to ride out his opening barrage. I'm amazed they have not backed their top batsman from the South African tour.
Stuart Clark must come in even if he is a bit rusty as he is probably still the best bowler of the lot and again I'm amazed he hasn't yet been picked when he was the leading bowler in the last Ashes series and on several other occasions. Brett Lee is not match fit and will probably be saved for the Oval, though his record in England, and indeed in his past few Test series is poor anyway so I don't see how he could make the team stronger when in less than full form and fitness.