Anelka doesn't suit the system France are playing. Tbh, the only player who does is Cisse. A genuine in the box goalscorer who likes to stay on the shoulder of the last defender. Anelka drops deep and likes to link up. When he tried to take players on, he failed because Uruguay had 3 defenders.
Domenech was heavily criticised by the commentators in that match but tbh, he did the right things. I don't know the reasoning as to why Diaby was played over Malouda, either because of the "bust up" or because Domenech realised the left becomes too congested. Either way it was the right move, you can't play your XI best players - you need to fit XI players in to the best system.
He also went with 1 striker rather than the standard 2 which was the right idea because Uruguay played 3 defenders. Against 3 defenders, 2 would be outplayed with the one free man picking up the left overs.
Govou offers a good balance to the side, playing as a defensive winger (similar to Kuyt and Liverpool) but against Uruguay who were sitting very deep and letting the game come to them, he wasn't necessary. I would've liked to see Valbuenas come on.
Uruguay just sat deep and played with a 5 man defence, they never really looked like wanting to win the game. Forlan and Suarez were isolated up top with no ball to play to wide players, forcing them to go wide themselves and making little impact.