Because when he first came to Inter he tried playing a 4-3-3 too(like he did at Chelsea and Porto), it didn't work out so he went for a 4-4-2 with a diamond midfield, then because he always liked to play with wide players, he shifted to a 4-2-3-1 in his second season at Inter.
His preferred formation has always been a 4-3-3, though on second thought, it would probably make more sense for him to play a 4-2-3-1 at Real Madrid too, so as to accommodate Kaka