at the end of the first movie, neo easily beats smith. but at the end of the third movie, neo gets his butt kicked by smith. is the smith in the last movie advanced or something? because neo kicked his butt in the first movie

The Smith in Revolutions is somehow MUCH more advanced than he was before having been deleted in the first film. There are a few factors that we have to consider. 1) After the first film, he is no longer apart of the system, so he has no restraints. 2) He refused to go to the Source after having been deleted, maybe he gained some strength in doing so. 3) By some odd feat, Smith has gained enough power to both clone himself and fly. He's probably become so powerful because Neo has gained just as much strength and an equal amount of abilities. We can't forget that they balance each other, so the stronger Neo gets, the stronger Smith gets, which was why they both had to be terminated in order for peace to be made.