Best of 3 imo.
Yes I clearly saw him run out-of-gas last year, the most obvious one for me was against Djokovic in the US Open : it was the first time I had seen him red faced, passive, as if he had been hurt by the heat ... which is exactly what happened to Djokovic in the past
(please note that I don't say he would have outplayed Djokovic without that : I think first two sets were very tight and Djokovic played better in 3rd set -and end of 2nd set- than in previous sets)
And he's often been used to great starts.
The question imo is more about the past : was it the best-of-5-format which was better for him as many people said or the fact that it was in grand slams then he was better prepared or more motivated ?
He said he felt more comfortable knowing that he could avoid in best-of-5 format the surprises which can happen from lower-ranked players in best-of-3 format :
every high-ranked player could say that, not esp Federer
Also he sometimes showed good stamina in the past (I think of his long match against Nadal in Roma 2006),
but you also know that his record in 5 setter-matches is not great : many explanations have been raised about that, but I wil ask another question : was his stamina that good ? for instance his bad 5th set in Aus open 2009 was it a mental explanation as many people said or could it also be explained by tiredness ?
I've even seen him lack stamina in 3rd set in best-of-3-matches !