I think you've pretty much got it right Mitchell1978. Don't think it's an injury-related fitness issue as Messi has shown numerous times in 2014 with his performances.
Also re: the conditions, yes they could be a factor but iirc Argentina infact have the most famous favourable conditions of all teams with all their games in the south of the country. Robben, for example, played the Mexico game in Fortaleza in 38 C heat with cooling breaks and managed to run 11383 m in 90 min, 3000 m more than Messi on average!
In the entire World Cup, Messi is the player that has one of the least distance covered per minute stat. He is 47th, the only players who covered less distance per min are 42 goalies and 4 defenders (Thiago Silva, Didier Zokora, Victor Bernardez and Godfrey Oboboana). When it comes to distance covered not in possession, he's the least in the entire World Cup after the goalies. Really don't think conditions or his role in the team etc. are relevant excuses.
Anyway, that amazing fivethirtyeight article (
Lionel Messi is impossible) shows Messi is by far the most efficient player on the planet, and here's another stat that can act as evidence.