In the city, bay didnt show us the Meg-Prime battle. You'd think that this was the whole purpose of the film, instead he spent his CGI money on that stupid "oops, my bad" scene that seemed to last forever. And yet, the Mission city battle felt just right. Prime vs Megatron, "one shall stand, one shall fall", Megatron was the threat he was supposed to be and he hauled ass, Ironhide shouting "it's starscream". In fact i got the sense that the decepticons were a threat and that made the fight more interesting.
The only good parts about the desert battle were:
1) Bumblebee vs constructicon (though the constr landed only one or two hits on Bee even though he was twice his size)
2) "Stwarsweeeam"
3) photography of the Fallen and Meg on the pyramid along with the fallen using his powers.
4) Jetfire and his axe
And yet i was so disappointed by Prime (too powerful, too brutal), by Devastator (getting owned by the twins for god's sake), by the Fallen... that it just didnt balance out well enough.
So Mission City wins it for me.